[med-svn] [phast] 01/02: Add manually edited manpages
Andreas Tille
tille at debian.org
Tue Sep 12 07:53:02 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository phast.
commit dfe6dcd47ea6f2c65d28cf3144377a408fbb9c91
Author: Andreas Tille <tille at debian.org>
Date: Tue Sep 12 09:52:05 2017 +0200
Add manually edited manpages
---
debian/changelog | 2 +-
debian/help2man/00_README | 9 +
debian/help2man/all_dists.1 | 29 ++
debian/help2man/base_evolve.1 | 49 +++
debian/help2man/chooseLines.1 | 13 +
debian/help2man/clean_genes.1 | 188 +++++++++++
debian/help2man/consEntropy.1 | 43 +++
debian/help2man/convert_coords.1 | 39 +++
debian/help2man/display_rate_matrix.1 | 86 ++++++
debian/help2man/dless.1 | 101 ++++++
debian/help2man/dlessP.1 | 41 +++
debian/help2man/draw_tree.1 | 25 ++
debian/help2man/eval_predictions.1 | 85 +++++
debian/help2man/exoniphy.1 | 222 +++++++++++++
debian/help2man/hmm_train.1 | 86 ++++++
debian/help2man/hmm_tweak.1 | 59 ++++
debian/help2man/hmm_view.1 | 33 ++
debian/help2man/indelFit.1 | 55 ++++
debian/help2man/indelHistory.1 | 43 +++
debian/help2man/maf_parse.1 | 172 +++++++++++
debian/help2man/makeHKY.1 | 32 ++
debian/help2man/modFreqs.1 | 19 ++
debian/help2man/msa_diff.1 | 31 ++
debian/help2man/msa_split.1 | 228 ++++++++++++++
debian/help2man/msa_view.1 | 378 +++++++++++++++++++++++
debian/help2man/pbsDecode.1 | 37 +++
debian/help2man/pbsEncode.1 | 30 ++
debian/help2man/pbsScoreMatrix.1 | 106 +++++++
debian/help2man/pbsTrain.1 | 157 ++++++++++
debian/help2man/phast.1 | 49 +++
debian/help2man/phastBias.1 | 172 +++++++++++
debian/help2man/phastCons.1 | 445 ++++++++++++++++++++++++++
debian/help2man/phastMotif.1 | 112 +++++++
debian/help2man/phastOdds.1 | 140 +++++++++
debian/help2man/phyloBoot.1 | 172 +++++++++++
debian/help2man/phyloFit.1 | 565 ++++++++++++++++++++++++++++++++++
debian/help2man/phyloP.1 | 305 ++++++++++++++++++
debian/help2man/prequel.1 | 201 ++++++++++++
debian/help2man/refeature.1 | 96 ++++++
debian/help2man/stringiphy.1 | 17 +
debian/help2man/treeGen.1 | 34 ++
debian/help2man/tree_doctor.1 | 151 +++++++++
debian/manpages | 1 +
debian/rules | 13 -
44 files changed, 4857 insertions(+), 14 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 3c64e44..edbb774 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,4 +2,4 @@ phast (1.4+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
- -- Andreas Tille <tille at debian.org> Fri, 27 May 2016 18:06:35 +0200
+ -- Andreas Tille <tille at debian.org> Tue, 12 Sep 2017 08:24:55 +0200
diff --git a/debian/help2man/00_README b/debian/help2man/00_README
new file mode 100644
index 0000000..e9c470a
--- /dev/null
+++ b/debian/help2man/00_README
@@ -0,0 +1,9 @@
+These manpages were once created for phast version 1.4 by using
+a patched help2man wrapper. This does not work reliably and
+thus the manpages are conserved here.
+
+Those manpages that are lacking the first line
+
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+
+where manually edited to some sensible layout.
diff --git a/debian/help2man/all_dists.1 b/debian/help2man/all_dists.1
new file mode 100644
index 0000000..1e5279c
--- /dev/null
+++ b/debian/help2man/all_dists.1
@@ -0,0 +1,29 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH ALL_DISTS "1" "May 2016" "all_dists 1.4" "User Commands"
+.SH NAME
+all_dists \- Given a tree in Newick (*.nh) format, report distances
+.SH DESCRIPTION
+Given a tree in Newick (*.nh) format, report distances
+between all pairs of leaves.
+If multiple files are given,
+then distances are computed by averaging across models,
+and statistics describing the errors in the estimates
+are reported (can be useful for bootstrapping; see
+\&'phyloBoot \fB\-\-dump\-mods\fR').
+.SH USAGE
+all_dists <tree.nh> [<tree2.nh> <tree3.nh>...]
+.SH OPTIONS
+.HP
+\fB\-\-mod\fR, \fB\-m\fR
+.IP
+Read from tree model (*.mod) file(s) instead of Newick file.
+.HP
+\fB\-\-tree\fR, \fB\-t\fR <file>|<string>
+.TP
+Use leaf names from given tree.
+Useful when primary files
+.IP
+use numbers rather than names.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+Print this help message.
diff --git a/debian/help2man/base_evolve.1 b/debian/help2man/base_evolve.1
new file mode 100644
index 0000000..d0d201d
--- /dev/null
+++ b/debian/help2man/base_evolve.1
@@ -0,0 +1,49 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH BASE_EVOLVE "1" "May 2016" "base_evolve 1.4" "User Commands"
+.SH NAME
+base_evolve \- Produce a synthetic alignment by simulating evolution according to
+.SH DESCRIPTION
+Produce a synthetic alignment by simulating evolution according to
+a phylogenetic model or a phylo\-HMM. Deals with base\-substitution
+only, not indels. If a multiple tree models are given, then an
+HMM file must be given showing how to transition between them.
+.SH EXAMPLE
+.IP
+base_evolve \fB\-\-nsites\fR 500 mytree.mod > simulated.fa
+.IP
+base_evolve \fB\-\-nsites\fR 500 simple\-gene.hmm tree1.mod tree2.mod \e
+tree3.mod \fB\-\-features\fR simulated2.gff \fB\-\-catmap\fR simple\-gene.cm \e
+> simulated2.fa
+.SH OPTIONS
+.HP
+\fB\-\-nsites\fR, \fB\-n\fR <nsites>
+Generate an alignment with <nsites> columns.
+Default is 1000.
+.HP
+\fB\-\-msa\-format\fR, \fB\-o\fR FASTA|PHYLIP|MPM|SS
+.TP
+Output alignment in specified format.
+Default is FASTA.
+.HP
+\fB\-\-features\fR, \fB\-f\fR <out.gff>
+(for use with a phylo\-HMM)
+Output an annotations file in GFF
+.IP
+reflecting the path through the phylo\-HMM.
+.HP
+\fB\-\-catmap\fR, \fB\-c\fR <map.cm>
+.TP
+(for use with \fB\-\-features\fR)
+Use specified category map to
+.IP
+define feature names.
+.HP
+\fB\-\-embed\fR, \fB\-e\fR <alt.mod>,<length>
+Embed an artificial element of the given length in the alignment,
+drawing columns from <alt.mod>. A single element is embedded in
+the exact middle of the generated alignment. Useful for testing
+sensitivity of methods for functional element detection.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Display this help message and exit.
diff --git a/debian/help2man/chooseLines.1 b/debian/help2man/chooseLines.1
new file mode 100644
index 0000000..881ac4b
--- /dev/null
+++ b/debian/help2man/chooseLines.1
@@ -0,0 +1,13 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH CHOOSELINES "1" "May 2016" "chooseLines 1.4" "User Commands"
+.SH NAME
+chooseLines \- Randomly choose k lines from a file of n lines, for 0 < k < n.
+.SH DESCRIPTION
+Randomly choose k lines from a file of n lines, for 0 < k < n.
+.SH USAGE
+chooseLines [OPTIONS] <infile>
+OPTIONS:
+\fB\-k\fR <k>
+Number of lines to choose (default is all lines).
+\fB\-h\fR
+Print this help message.
diff --git a/debian/help2man/clean_genes.1 b/debian/help2man/clean_genes.1
new file mode 100644
index 0000000..416ee0f
--- /dev/null
+++ b/debian/help2man/clean_genes.1
@@ -0,0 +1,188 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH CLEAN_GENES "1" "May 2016" "clean_genes 1.4" "User Commands"
+.SH NAME
+clean_genes \- Given a GFF describing a set of genes and a corresponding
+.SH DESCRIPTION
+Given a GFF describing a set of genes and a corresponding
+multiple alignment, output a new GFF with only those
+genes that meet certain "cleanliness" criteria. The
+coordinates in the GFF are assumed to correspond to
+the reference sequence in the alignment, which is
+assumed to be the first one listed. Default behavior
+is simply to require that all annotated start/stop codons and
+splice sites are valid in the reference sequence (GT\-AG,
+GC\-AG, and AT\-AC splice sites are allowed). This can
+be used with an "alignment" consisting of a single
+sequence to filter out incorrect annotations. Options
+are available to impose additional criteria as well,
+mostly having to do with conservation across species
+(see the '\-\-conserved' option in particular).
+.SH SYNOPSIS
+clean_genes [options] <gff_fname> <msa_fname>
+.SH OPTIONS
+.HP
+\fB\-\-start\fR, \fB\-s\fR
+.IP
+Require conserved start codons (all species)
+.HP
+\fB\-\-stop\fR, \fB\-t\fR
+.IP
+Require conserved stop codons (all species)
+.HP
+\fB\-\-splice\fR, \fB\-l\fR
+.TP
+Require conserved splice sites (all species).
+By default,
+.IP
+only GT\-AG, GC\-AG, and AT\-AC splice sites are allowed (see also
+\fB\-\-splice\-strict\fR)
+.HP
+\fB\-\-fshift\fR, \fB\-f\fR
+.TP
+Require that no frame\-shift gap is present in any species.
+Frame
+.TP
+shifts are evaluated with respect to the reference sequence.
+Gaps
+.IP
+that have non\-multiple\-of\-three lengths are allowed if
+compensatory gaps occur nearby (see source code for details).
+.HP
+\fB\-\-nonsense\fR, \fB\-n\fR
+.IP
+Require that no premature stop codon is present in any species.
+.HP
+\fB\-\-conserved\fR, \fB\-c\fR
+.IP
+Implies \fB\-\-start\fR, \fB\-\-stop\fR, \fB\-\-splice\fR, \fB\-\-fshift\fR, and \fB\-\-nonsense\fR.
+Recommended option for cross\-species analysis.
+.HP
+\fB\-\-N\-limit\fR, \fB\-N\fR <f>
+.IP
+Maximum fraction of bases aligned to CDSs that are Ns in any
+species (<f> must be between 0 and 1). Default is 0.05. Set to 1
+to allow any number of Ns.
+.HP
+\fB\-\-clean\-gaps\fR, \fB\-e\fR
+.TP
+Require all cds gaps to be multiples of three in length.
+Can be
+.IP
+used with \fB\-\-conserved\fR.
+.HP
+\fB\-\-indel\-strict\fR, \fB\-I\fR
+.TP
+Implies \fB\-\-clean_gaps\fR, usually used with \fB\-\-conserved\fR.
+Prohibits
+.IP
+overlapping cds gaps in different sequences, gaps near cds
+boundaries, and gaps in the reference sequence within and between
+flanking features (splice sites, etc.; see code for details).
+Designed for use in training a phylo\-HMM with an indel model.
+.HP
+\fB\-\-splice\-strict\fR, \fB\-C\fR
+.TP
+Implies \fB\-\-splice\fR.
+Allow only GT\-AG canonical splice sites. Useful
+.IP
+when training a gene finder with a simple model for splice sites.
+.HP
+\fB\-\-groupby\fR, \fB\-g\fR <tag>
+.IP
+Group features according to specified tag (default
+"transcript_id"). If any feature within a group fails, the
+entire group will be discarded. By choosing to group features
+according to different criteria, you can make the program
+"clean" the data set at different levels. For example, to
+clean at the level of individual exons, add a tag like
+"exon_id" to indicate exons (see the program "refeature"),
+and then invoke clean_genes with "\-\-groupby exon_id".
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
+.TP
+Alignment file format.
+Default is to guess format from file
+.IP
+contents.
+.HP
+\fB\-\-refseq\fR, \fB\-r\fR <seqfile.fa>
+.TP
+(Required with \fB\-\-msa\-format\fR MAF)
+Complete reference
+.IP
+sequence for alignment (FASTA format).
+.HP
+\fB\-\-offset5\fR, \fB\-o\fR <n>
+.TP
+(Default 0)
+Offset of canonical "GT" with respect to boundary
+.TP
+on *intron side* of annotated 5' splice sites.
+Useful with
+.IP
+annotations that describe a window around the canonical splice site.
+.HP
+\fB\-\-offset3\fR, \fB\-p\fR <n>
+.TP
+(Default 0)
+Offset of canonical "AG" with respect to boundary
+.IP
+on intron side of annotated 3' splice sites.
+.HP
+\fB\-\-log\fR, \fB\-L\fR <fname>
+.IP
+Write human\-readable log to specified file.
+.HP
+\fB\-\-machine\-log\fR, \fB\-M\fR <fname>
+.IP
+Like \fB\-\-log\fR, but produces more concise, machine\-readable log.
+.HP
+\fB\-\-stats\fR, \fB\-S\fR <fname>
+.IP
+Write statistics on retained and discarded features to specified file.
+.HP
+\fB\-\-discards\fR, \fB\-d\fR <fname>
+.IP
+Write discarded features to specified file.
+.HP
+\fB\-\-no\-output\fR, \fB\-x\fR
+.TP
+Suppress output of "cleaned" features to stdout.
+Useful if only
+.IP
+log file and/or stats are of interest.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
+.PP
+NOTES: Feature types are defined as follows.
+.TP
+coding exon
+<\-> "CDS"
+.TP
+start codon
+<\-> "start_codon"
+.TP
+stop codon
+<\-> "stop_codon"
+.IP
+5' splice site <\-> "5'splice"
+3' splice site <\-> "3'splice"
+.IP
+In addition, splice sites in UTR can be separately designated as
+"5'splice_utr" and "3'splice_utr". Errors in these sites will be
+given a different code in the log files, which can be useful for
+tracking purposes.
+.IP
+If evaluation is done at the level of individual exons (see
+\fB\-\-groupby\fR), then splice sites are considered independently
+rather than in the context of introns. As a result, the exons flanking
+a GT\-AC or AT\-AG intron might (misleadingly) be considered "clean".
+.IP
+With \fB\-\-fshift\fR and \fB\-\-nonsense\fR, it is possible for entries
+to pass through that have stop codons in the frame of the
+*reference* sequence, although they do not have any in their
+own frame. Use \fB\-\-clean\-gaps\fR instead to guarantee that no stop
+codons occur in any sequence in the frame of the reference
+sequence.
diff --git a/debian/help2man/consEntropy.1 b/debian/help2man/consEntropy.1
new file mode 100644
index 0000000..d1a5518
--- /dev/null
+++ b/debian/help2man/consEntropy.1
@@ -0,0 +1,43 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH CONSENTROPY "1" "May 2016" "consEntropy 1.4" "User Commands"
+.SH NAME
+consEntropy \- For use with phastCons. Given phylogenetic models for conserved and
+.SH DESCRIPTION
+For use with phastCons.
+Given phylogenetic models for conserved and
+.IP
+non\-conserved states, the target coverage, and the (prior) expected
+length of a conserved element, compute the relative entropy (H) of the
+phylogenetic models, the expected minimum number of conserved sites
+required to predict conserved element (L_min), the "phylogenetic
+information threshold" (PIT = L_min * H), and the expected maximum
+number of nonconserved sites tolerated within a conserved element
+(L_max). Also will make a recommendation for a new prior expected
+length based on a given target value of L_min*H (see \fB\-\-LminH\fR).
+.SH SYNOPSIS
+consEntropy [OPTIONS] <target\-coverage> <expected\-length> \e
+.IP
+[ <cons.mod> <noncons.mod> ]
+.SH OPTIONS
+.HP
+\fB\-\-H\fR, \fB\-H\fR <value>
+.IP
+Instead of computing the relative entropy from two .mod files,
+just use the specified value. The .mod files aren't required
+in this case.
+.HP
+\fB\-\-LminH\fR, \fB\-L\fR <value> [or \fB\-\-NH\fR/\-N, for backward compatibility]
+.IP
+Report the expected length that would produce the specified value
+of L_min * H (i.e., the specified PIT), assuming H remains constant
+(it generally won't). Can be used iteratively to converge on a
+desired PIT.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
+.SS "NOTE:"
+.IP
+The relative entropy is currently computed by brute force, i.e.,
+by enumerating all possible labelings of the leaves of the tree.
+This approach won't be feasible with large trees.
diff --git a/debian/help2man/convert_coords.1 b/debian/help2man/convert_coords.1
new file mode 100644
index 0000000..e2c3e87
--- /dev/null
+++ b/debian/help2man/convert_coords.1
@@ -0,0 +1,39 @@
+.TH CONVERT_COORDS "1" "May 2016" "convert_coords 1.4" "User Commands"
+.SH NAME
+convert_coords \- converts coordinates of features in a GFF file according to a multiple alignment
+.SH DESCRIPTION
+Converts coordinates of features in a GFF file according to a multiple
+alignment. Will map from the coordinate system of any sequence to any
+other sequence; can also map to or from the coordinate system of the
+entire alignment. In addition, supports translation of coordinates by
+specified offset.
+.SH OPTIONS
+.TP
+\fB\-m\fR <msa_fname>
+(required) Name of file in which alignment is defined.
+.TP
+\fB\-f\fR <gff_fname>
+(required) Name of file in which features are defined (GFF).
+.TP
+\fB\-s\fR <src_frame>
+Index of frame of reference for feature coordinates, as
+defined in the GFF file. Use an integer 1\-N (if N seqs)
+or 0 to indicate the coordinate system of the alignment
+as a whole. Default behavior is to match features with
+alignment sequences by name (feature by feature).
+\fB\-d\fR <dest_frame> Index of destination frame of reference.
+Default is 0
+(whole MSA).
+\fB\-p\fR <coord_off>
+Positive coordinate offset. This value will be
+added to all coordinates. Useful when
+the alignment (or sequence) for which the coordinates
+are specified is a sub\-alignment of yours.
+\fB\-n\fR <coord_off>
+Negative coordinate offset. This value will be
+subtracted from all coordinates. Useful when your
+alignment is a sub\-alignment of the alignment (or
+sequence) for which the coordinates are specified.
+\fB\-i\fR FASTA|PHYLIP|MPM|SS
+Alignment format. Default is to guess format from file
+contents
diff --git a/debian/help2man/display_rate_matrix.1 b/debian/help2man/display_rate_matrix.1
new file mode 100644
index 0000000..aa85c78
--- /dev/null
+++ b/debian/help2man/display_rate_matrix.1
@@ -0,0 +1,86 @@
+.TH DISPLAY_RATE_MATRIX "1" "May 2016" "display_rate_matrix 1.4" "User Commands"
+.SH NAME
+display_rate_matrix \- this tool is part of the PHAST suite
+.SH OPTIONS
+.TP
+\fB\-t\fR <t>: Output P(t) = exp(Qt) instead of Q.
+Requires t >= 0.
+.IP
+Use "\-t A" to output a matrix for each branch of the tree.
+.TP
+\fB\-f\fR:
+Show equilibrium frequencies as an additional table row.
+In list node they are shown with first tuple being \-.
+.TP
+\fB\-e\fR:
+Show "exchangeabilities" instead of raw matrix elements
+(that is, divide each element by the equilibrium frequency
+of its column). Not available with \fB\-t\fR.
+.TP
+\fB\-d\fR:
+Suppress printing of elements on main diagonal.
+.TP
+\fB\-L\fR:
+Format table for typesetting with LATEX. Incompatible with \fB\-l\fR.
+.TP
+\fB\-l\fR:
+Show matrix elements as a list rather than as a table.
+When \fB\-t\fR is not specified (rate matrix case), only off\-diagonal
+elements will be printed.
+.TP
+\fB\-i\fR:
+(For use with \fB\-l\fR only) Report whether each substitution is
+a transition or a transversion.
+.TP
+\fB\-z\fR:
+(For use with \fB\-l\fR) Report elements equal to zero (omitted by
+default, except with \fB\-t\fR). Implied by \fB\-a\fR.
+.TP
+\fB\-S\fR:
+(For use with \fB\-l\fR) Assume a symmetric matrix and report half
+as many lines. Useful with \fB\-e\fR.
+.TP
+\fB\-E\fR:
+(for use with \fB\-l\fR) Print rates and probabilities
+in scientific notation (format %e instead of %f).
+.TP
+\fB\-a\fR:
+(Requires a model of order 3). Replace a matrix of codon
+substitution rates with the induced matrix of amino acid
+substitution rates, according to the universal genetic
+code. See Yang, Nielsen, and Hasegawa, 1998.
+.TP
+\fB\-s\fR:
+(For use with \fB\-a\fR) Include stop codons (by default suppressed).
+.HP
+\fB\-M\fR <f>: (For use with \fB\-l\fR only; implies \fB\-a\fR) Read an amino\-acid
+.IP
+substitution matrix from file <f> and report values from
+this matrix with the induced amino acid substitution rates.
+Matrix should be in the format used by BLAST (as
+produced by the NCBI "pam" program)
+.TP
+\fB\-N\fR <f>
+Like \fB\-M\fR but for matrices in the format used by the PAML
+package for amino acid substitution and rate matrices.
+.TP
+\fB\-A\fR <f>: (For use with \fB\-l\fR only and not with \fB\-M\fR/\-N)
+Read alternative
+.IP
+substitution scores from file <f> and report values in
+output. File <f> should have three columns: a "from"
+tuple, a "to" tuple, and a real\-valued score.
+Substitutions not listed will be given null scores and
+reported as "NA".
+.TP
+\fB\-B\fR <f>
+Like \fB\-A\fR but compares to rates of a single\-nucleotide model
+(order 1). File <f> should be a standard tree model (.mod) file.
+.TP
+\fB\-C\fR
+Report context\-dependent transition/transversion rates, as
+shown in Tables 2 and 3 of Morton et al., JME 45:227\-231, 1997.
+Requires a model of order 3 with a DNA alphabet.
+.TP
+\fB\-h\fR
+Print this help message.
diff --git a/debian/help2man/dless.1 b/debian/help2man/dless.1
new file mode 100644
index 0000000..1d31145
--- /dev/null
+++ b/debian/help2man/dless.1
@@ -0,0 +1,101 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH DLESS "1" "May 2016" "dless 1.4" "User Commands"
+.SH NAME
+dless \- Attempts to identify elements under selection in all species or in
+.SH DESCRIPTION
+Attempts to identify elements under selection in all species or in
+some subset of species, based on a multiple alignment and a
+phylo\-HMM. In particular, detects elements that have been under
+selection since the divergence of all species in the given set,
+that were "born" on some branch of the tree since their divergence
+and have been under selection since, or that were present in the
+common ancestor but "died" (ceased to be under selection) on some
+branch of the tree. Currently only detects negative selection,
+but extensions to detect positive selection as well are planned.
+.SH EXAMPLE
+.SH OPTIONS
+.HP
+\fB\-\-rho\fR, \fB\-R\fR <rho>
+.IP
+(default 0.3)
+.HP
+\fB\-\-transitions\fR, \fB\-t\fR [~]<mu>,<nu>
+.IP
+Set the transition probabilities of the two\-state HMM using
+the specified values of <mu> and <nu> (both between 0 and 1).
+.HP
+\fB\-\-phi\fR, \fB\-p\fR [~]<phi>
+.IP
+(default 0.5)
+.HP
+\fB\-\-target\-coverage\fR, \fB\-C\fR [~]<gamma>
+.IP
+(Alternative to transitions, use with \fB\-\-expected\-length\fR) Set
+the transition parameters such that the expected fraction of
+sites in conserved elements is <gamma> (betwen 0 and 1). This
+is a *prior* rather than *posterior* expectation and assumes
+stationarity of the state\-transition process. This option
+causes the ratio mu/nu to be fixed at (1\-gamma)/gamma, and
+together with \fB\-\-expected\-length\fR, completely defines the
+transition probabilities.
+.HP
+\fB\-\-expected\-length\fR, \fB\-E\fR [~]<omega>
+.IP
+(Alternative to \fB\-\-transitions\fR, use with \fB\-\-target\-coverage\fR) Set
+transition probabilities such that the (prior) expected length
+of a conserved element is <omega>. The parameter mu is set to
+1/omega.
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
+.IP
+Alignment format (default is to guess format from file contents).
+Note that the program msa_view can be used for conversion.
+.HP
+\fB\-\-refseq\fR, \fB\-M\fR <fname>
+.IP
+(for use with \fB\-\-msa\-format\fR MAF) Read the complete text of the
+reference sequence from <fname> (FASTA format) and combine it
+with the contents of the MAF file to produce a complete,
+ordered representation of the alignment. The reference
+sequence of the MAF file is assumed to be the one that appears
+first in each block.
+.HP
+\fB\-\-refidx\fR, \fB\-r\fR <refseq_idx>
+Use coordinate frame of specified sequence in output.
+Default
+.IP
+value is 1, first sequence in alignment; 0 indicates
+coordinate frame of entire multiple alignment.
+.HP
+\fB\-\-seqname\fR, \fB\-N\fR <name>
+Use specified string for 'seqname' (GFF) or 'chrom' field in
+output file. Default is obtained from input file name (double
+filename root, e.g., "chr22" if input file is "chr22.35.ss").
+.HP
+\fB\-\-idpref\fR, \fB\-P\fR <name>
+Use specified string as prefix of generated ids in output
+file. Can be used to ensure ids are unique. Default is
+obtained from input file name (single filename root, e.g.,
+"chr22.35" if input file is "chr22.35.ss").
+.HP
+\fB\-\-indel\-model\fR, \fB\-I\fR alpha,beta,tau[,alpha2,beta2,tau2]
+.IP
+Use a simple model of insertions and deletions that assumes a known
+indel history and at most one indel per branch of the tree at any
+given position. The parameters alpha and beta are rates of
+insertion and deletion, respectively, per expected substitution per
+site, and the parameter tau is approximately the inverse of the
+expected indel length (see indelFit). If two sets are parameters
+are given the first will be used for nonconserved regions and the
+second for conserved regions. If \fB\-\-indel\-history\fR is not used, a
+history will be inferred on the fly using a simple parsimony
+algorithm.
+.HP
+\fB\-\-indel\-history\fR, \fB\-H\fR <file.ih>
+.IP
+(for use with \fB\-\-indel\-model\fR) Use the specified indel history (see
+indelHistory).
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Show this help message and exit.
diff --git a/debian/help2man/dlessP.1 b/debian/help2man/dlessP.1
new file mode 100644
index 0000000..9a87647
--- /dev/null
+++ b/debian/help2man/dlessP.1
@@ -0,0 +1,41 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH DLESSP "1" "May 2016" "dlessP 1.4" "User Commands"
+.SH NAME
+dlessP \- Computes various p-values and other stats of interest for dless
+.SH DESCRIPTION
+Computes various p\-values and other stats of interest for dless
+predictions and writes them to a tab\-delimited file. The 'alignment'
+and 'tree.mod' arguments should be as given to DLESS, and
+\&'predictions.gff' should be the output of DLESS.
+.SH OPTIONS
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
+.IP
+Alignment format (default is to guess format from file contents).
+Note that the program msa_view can be used for conversion.
+.HP
+\fB\-\-refseq\fR, \fB\-M\fR <fname>
+(for use with \fB\-\-msa\-format\fR MAF) Read the complete text of the
+reference sequence from <fname> (FASTA format) and combine it
+with the contents of the MAF file to produce a complete,
+ordered representation of the alignment. The reference
+sequence of the MAF file is assumed to be the one that appears
+first in each block.
+.HP
+\fB\-\-refidx\fR, \fB\-r\fR <refseq_idx>
+Use coordinate frame of specified sequence in output.
+Default
+value is 1, first sequence in alignment; 0 indicates
+coordinate frame of entire multiple alignment.
+.HP
+\fB\-\-timing\fR, \fB\-t\fR <file>
+.IP
+Write timing data to <file>.
+.HP
+\fB\-\-html\fR, \fB\-H\fR <dirname>
+Create a directory and write one HTML file into it per DLESS
+prediction, giving the stats for that prediction.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Show this help message and exit.
diff --git a/debian/help2man/draw_tree.1 b/debian/help2man/draw_tree.1
new file mode 100644
index 0000000..319044a
--- /dev/null
+++ b/debian/help2man/draw_tree.1
@@ -0,0 +1,25 @@
+.TH DRAW_TREE "1" "May 2016" "draw_tree 1.4" "User Commands"
+.SH NAME
+draw_tree \- Produces a simple postscript rendering of a tree
+.SH SYNOPSIS
+draw_tree [\-dbvs] <tree.nh>|<tree.mod>
+.SH OPTIONS
+.TP
+<tree_fname>
+(Required) File name of tree (expected to be in
+Newick format, unless filename ends with '.mod', in
+which case expected to be a tree model file).
+.TP
+\fB\-d\fR
+Print "diagonal" branches, instead of "right\-angle" or
+"square" ones (produces a "cladogram", as opposed to a
+"phenogram"). This option implies \fB\-s\fR.
+.TP
+\fB\-b\fR
+Suppress branch lengths.
+.TP
+\fB\-v\fR
+Vertical layout.
+.TP
+\fB\-s\fR
+Don't draw branches to scale.
diff --git a/debian/help2man/eval_predictions.1 b/debian/help2man/eval_predictions.1
new file mode 100644
index 0000000..a2e41d5
--- /dev/null
+++ b/debian/help2man/eval_predictions.1
@@ -0,0 +1,85 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH EVAL_PREDICTIONS "1" "May 2016" "eval_predictions 1.4" "User Commands"
+.SH NAME
+eval_predictions \- Compares predicted genes with "real" (or annotated) genes.
+.SH SYNOPSIS
+.B eval_predictions
+\fB\-r\fR <real_fname_list> \fB\-p\fR <pred_fname_list>
+\fB\-l\fR <seq_len_list> [OPTIONS]
+.SH DESCRIPTION:
+Compares predicted genes with "real" (or annotated) genes.
+Reports standard measures of prediction quality. The following
+measures are reported:
+.IP
+\- nucleotide sensitivity (Sn)
+.IP
+\- nucleotide specificity (Sp)
+.IP
+\- approximate correlation (AC)
+.IP
+\- correlation coefficient (CC)
+.IP
+\- exon sensitivity (ESn)
+.IP
+\- exon specificity (ESp)
+.IP
+\- proportion of real exons correctly predicted (CRa)
+.IP
+\- proportion of real exons partially predicted (PCa)
+.IP
+\- proportion of real exons with overlapping predictions (OLa)
+.IP
+\- missed exons (ME)
+.IP
+\- proportion of predicted exons that are correct (CRp)
+.IP
+\- proportion of predicted exons that are partially correct (PCp)
+.IP
+\- proportion of predicted exons that overlap real ones (OLp)
+.IP
+\- wrong exons (WE)
+.PP
+All quantities are computed as described in "Evaluation of Gene\-Finding
+Programs on Mammalian Sequences," by Rogic et al. (Genome Research
+11:817\-832). Note that CRa + PCa + OLa + ME = 1 and CRp + PCp + OLp +
+WE = 1. Note also that each set (predicted and real) should consist of
+non\-overlapping groups of features (see 'refeature').
+.SH OPTIONS
+.HP
+\fB\-r\fR <real_fname_list>
+.IP
+(required) List of names of files defining real genes (GFF).
+.HP
+\fB\-p\fR <pred_fname_list>
+.IP
+(required) List of names of files defining predicted genes
+(GFF). Must correspond in order to <real_fname_list>.
+.HP
+\fB\-l\fR <seq_len_list>
+(required) List of lengths of sequences.
+Needed to compute
+.IP
+certain nucleotide\-level statistics.
+.HP
+\fB\-f\fR <feat_list>
+.TP
+List of names of all features denoting exon regions.
+By
+.IP
+default, equal to the single name "CDS".
+.HP
+\fB\-d\fR <fname_prefix>
+Dump full coords of correct, partially correct, wrong, missed,
+and overlapping exons to a set of files having the specified
+file name prefix.
+.HP
+\fB\-n\fR <nbases>
+Also report stats on "nearly correct" exons, that is, incorrect
+exons whose boundaries are within <nbases> of being correct.
+Columns will be labeled "NCa" and "NCp".
+.HP
+\fB\-h\fR
+Print this help message.
+.PP
+NOTE: be sure stop codons are included in CDSs in both the predicted
+and real sets, or in neither set.
diff --git a/debian/help2man/exoniphy.1 b/debian/help2man/exoniphy.1
new file mode 100644
index 0000000..8e8ec57
--- /dev/null
+++ b/debian/help2man/exoniphy.1
@@ -0,0 +1,222 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH EXONIPHY "1" "May 2016" "exoniphy 1.4" "User Commands"
+.SH NAME
+exoniphy \- Prediction of evolutionarily conserved protein-coding exons using
+Required argument <msa_fname> must be a multiple alignment
+file, in one of several possible formats (see \fB\-\-msa\-format\fR).
+.SH DESCRIPTION
+Prediction of evolutionarily conserved protein\-coding exons using
+a phylogenetic hidden Markov model (phylo\-HMM). By default, a
+model definition and model parameters are used that are
+appropriate for exon prediction in human DNA, based on
+human/mouse/rat alignments and a 60\-state HMM. Using the \fB\-\-hmm\fR,
+\fB\-\-tree\-models\fR, and \fB\-\-catmap\fR options, however, it is possible to
+define alternative phylo\-HMMs, e.g., for different sets of species
+and different phylogenies, or for prediction of exon pairs or
+complete gene structures.
+.SH OPTIONS
+.IP
+(Model definition and model parameters)
+.HP
+\fB\-\-hmm\fR, \fB\-H\fR <fname>
+.IP
+Name of HMM file defining states and transition probabilities.
+By default, the 60\-state HMM described in Siepel & Haussler
+(2004) is used, with transition probabilities appropriate for
+mammalian genomes (estimated as described in that paper).
+.HP
+\fB\-\-tree\-models\fR, \fB\-m\fR <fname_list>
+List of tree model (*.mod) files, one for each state in the
+HMM. Order of models must correspond to order of states in
+HMM file. By default, a set of models appropriate for human,
+mouse, and rat are used (estimated as described in Siepel &
+Haussler, 2004).
+.HP
+\fB\-\-catmap\fR, \fB\-c\fR <fname>|<string>
+.TP
+Mapping of feature types to category numbers.
+Can give either
+.IP
+a filename or an "inline" description of a simple category
+map, e.g., \fB\-\-catmap\fR "NCATS = 3 ; CDS 1\-3". By default, a
+category map is used that is appropriate for the 60\-state HMM
+mentioned above.
+.HP
+\fB\-\-extrapolate\fR, \fB\-e\fR <phylog.nh> | default
+Extrapolate to a larger set of species based on the given
+phylogeny (Newick\-format). The trees in the given tree models
+(*.mod files) must be subtrees of the larger phylogeny. For
+each tree model M, a copy will be created of the larger
+phylogeny, then scaled such that the total branch length of
+the subtree corresponding to M's tree equals the total branch
+length of M's tree; this new version will then be used in
+place of M's tree. (Any species name present in this tree but
+not in the data will be ignored.) If the string "default"
+is given instead of a filename, then a phylogeny for 25
+vertebrate species, estimated from sequence data for Target 1
+(CFTR) of the NISC Comparative Sequencing Program (Thomas et
+al., 2003), will be assumed.
+.HP
+\fB\-\-data\-path\fR, \fB\-D\fR <path>
+.IP
+Path to the directory with phast data. Exoniphy default models should
+be in <path>/exoniphy/. Default is set at compile time.
+.IP
+(Input and output)
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
+.TP
+File format of input alignment.
+Default is to guess alignment
+.IP
+format from file contents.
+.HP
+\fB\-\-score\fR, \fB\-S\fR
+Report log\-odds scores for predictions, equal to their log
+total probability under an exon model minus their log total
+probability under a background model. The exon model can be
+altered using \fB\-\-cds\-types\fR and \fB\-\-signal\-types\fR and the
+background model can be altered using \fB\-\-backgd\-types\fR (see below).
+.HP
+\fB\-\-seqname\fR, \fB\-s\fR <name>
+.IP
+Use specified string as "seqname" field in GFF output.
+Default is obtained from input file name (double filename
+root, e.g., "chr22" if input file is "chr22.35.ss").
+.HP
+\fB\-\-idpref\fR, \fB\-p\fR <name>
+.IP
+Use specified string as prefix of generated ids in GFF output.
+Can be used to ensure ids are unique. Default is obtained
+from input file name (single filename root, e.g., "chr22.35"
+if input file is "chr22.35.ss").
+.HP
+\fB\-\-grouptag\fR, \fB\-g\fR <tag>
+Use specified string as the tag denoting groups in GFF output
+(default is "transcript_id").
+.HP
+\fB\-\-alias\fR, \fB\-A\fR <alias_def>
+.IP
+Alias names in input alignment according to given definition,
+e.g., "hg17=human; mm5=mouse; rn3=rat". Useful with default
+tree models and with \fB\-\-extrapolate\fR. (Default models
+use generic common names such as "human", "mouse", and
+"rat". This option allows a mapping to be established
+between the leaves of trees in these files and the sequences
+of an alignment that uses an alternative naming convention.)
+.IP
+(Altering the states and transition probabilities of the HMM)
+.HP
+\fB\-\-no\-cns\fR, \fB\-x\fR
+.IP
+Eliminate the state/category for conserved noncoding sequence
+from the default HMM and category map. Ignored if non\-default
+HMM and category map are selected.
+.HP
+\fB\-\-reflect\-strand\fR, \fB\-U\fR
+.IP
+Given an HMM describing the forward strand, create a larger
+HMM that allows for features on both strands by "reflecting"
+the HMM about all states associated with background categories
+(see \fB\-\-backgd\-cats\fR). The new HMM will be used for predictions
+on both strands. If the default HMM is used, then this option
+will be used automatically.
+.HP
+\fB\-\-bias\fR, \fB\-b\fR <val>
+.IP
+Set "coding bias" equal to the specified value (default
+\fB\-3\fR.33 if default HMM is used, 0 otherwise). The coding bias
+is added to the log probabilities of transitions from
+background states to non\-background states (see
+\fB\-\-backgd\-cats\fR), then all transition probabilities are
+renormalized. If the coding bias is positive, then more
+predictions will tend to be made and sensitivity will tend to
+improve, at some cost to specificity; if it is negative, then
+fewer predictions will tend to be made, and specificity will
+tend to improve, at some cost to sensitivity.
+.HP
+\fB\-\-sens\-spec\fR, \fB\-Y\fR <fname\-root>
+Make predictions for a range of different coding
+biases (see \fB\-\-bias\fR), and write results to files with given
+filename root. This allows the sensitivity/specificity
+tradeoff to be examined. The range is fixed at \fB\-20\fR to 10,
+and 10 different sets of predictions are produced.
+(Feature types)
+.HP
+\fB\-\-backgd\-types\fR, \fB\-B\fR <list>
+.IP
+Feature types to be considered "background" (default value:
+"background,CNS"). Affects \fB\-\-reflect\-strand\fR,
+\fB\-\-score\fR, and \fB\-\-bias\fR.
+.HP
+\fB\-\-cds\-types\fR, \fB\-C\fR <list>
+.IP
+(for use with \fB\-\-score\fR) Feature types that represent protein\-coding
+regions (default value: "CDS").
+.HP
+\fB\-\-signal\-types\fR, \fB\-L\fR <list>
+(for use with \fB\-\-score\fR) Types of features to be considered
+"signals" during scoring (default value:
+"start_codon,stop_codon,5'splice,3'splice,prestart,cds5'ss,cds3'ss").
+One score is produced for a CDS feature (as defined by
+\fB\-\-cds\-types\fR) and the adjacent signal features; the score is
+then assigned to the CDS feature.
+.IP
+(Indels)
+.HP
+\fB\-\-indels\fR, \fB\-I\fR
+.IP
+Use the indel model described in Siepel & Haussler (2004).
+.HP
+\fB\-\-no\-gaps\fR, \fB\-W\fR <list>
+Prohibit gaps in sites of the specified categories (gaps result in
+emission probabilities of zero). If the default category map
+is used (see \fB\-\-catmap\fR), then gaps are prohibited in start and
+stop codons and at the canonical GT and AG positions of splice
+sites (with or without \fB\-\-indels\fR). In all other cases, the
+default behavior is to treat gaps as missing data, or to address
+them with the indel model (\fB\-\-indels\fR).
+.HP
+\fB\-\-require\-informative\fR, \fB\-N\fR <list>
+.IP
+Require "informative" columns (i.e., columns with more than
+two non\-missing\-data characters, excluding sequences specified
+by \fB\-\-not\-informative\fR) in the given categories (list by name
+or number). Non\-informative columns will be given emission
+probabilities of zero. If the default category map is used
+(see \fB\-\-catmap\fR), then this option applies automatically to
+CDSs, start and stop codons, and the canonical GT and AG
+positions of splice sites. Note that alignment gaps *are*
+considered informative; the way they are handled is defined by
+\fB\-\-indels\fR and \fB\-\-no\-gaps\fR.
+.HP
+\fB\-\-not\-informative\fR, \fB\-n\fR <list>
+.IP
+Do not consider the specified sequences (listed by name) when
+deciding whether a column is informative. This option can be
+useful when sequences are present that are very close to the
+reference sequence and thus do not contribute much in the way
+of phylogenetic information. E.g., one might use
+"\-\-not\-informative chimp" with a human\-referenced multiple
+alignment including chimp sequence.
+.IP
+(Other)
+.HP
+\fB\-\-quiet\fR, \fB\-q\fR
+.IP
+Proceed quietly (without messages to stderr).
+.HP
+\fB\-\-help\fR \fB\-h\fR
+Print this help message.
+.PP
+REFERENCES:
+A. Siepel and D. Haussler.
+2004. Computational identification of
+evolutionarily conserved exons.
+Proc. 8th Annual Int'l Conf.
+.IP
+on Research in Computational Biology (RECOMB '04), pp. 177\-186.
+J. Thomas et al.
+2003. Comparative analyses of multi\-species
+sequences from targeted genomic regions.
+Nature 424:788\-793.
diff --git a/debian/help2man/hmm_train.1 b/debian/help2man/hmm_train.1
new file mode 100644
index 0000000..d8f2f97
--- /dev/null
+++ b/debian/help2man/hmm_train.1
@@ -0,0 +1,86 @@
+.TH HMM_TRAIN "1" "May 2016" "hmm_train 1.4" "User Commands"
+.SH NAME
+hmm_train \- Estimate the transition probabilities of an HMM, based on multiple
+\fB\-g\fR <gff_fname_list> [OPTIONS] > out.hmm
+.SH "DESCRIPTION:"
+Estimate the transition probabilities of an HMM, based on multiple
+alignments, sequence annotations, and a category map.
+.SH OPTIONS
+.SS required options
+.HP
+\fB\-m\fR <msa_fname_list>
+.IP
+List of multiple sequence alignment files.
+Currently, in testing mode, the list must be of length one.
+.HP
+\fB\-c\fR <category_map_fname>
+.IP
+File defining mapping of feature types to category
+numbers.
+.HP
+\fB\-g\fR <gff_fname_list>
+.IP
+Files in GFF defining sequence
+features to be used in labeling sites. Frame of reference of
+feature indices is determined feature\-by\-feature according to
+.TP
+\&'seqname' attribute.
+Filenames must correspond in number and order
+.IP
+to the elements of <msa_fname_list>.
+.SS alignment options
+.HP
+\fB\-M\fR <msa_length_list>
+.IP
+(Mutually exclusive with \fB\-m\fR) Assume alignments
+of the specified lengths (comma\-separated list) and do not not
+attempt to map the coordinates in the specified GFFs (assume
+they are in the desired coordinate frame). This option allows
+an HMM to be trained directly from GFFs, without alignments.
+Not permitted with \fB\-I\fR.
+.HP
+\fB\-i\fR PHYLIP|FASTA|MPM|SS
+.IP
+(default SS) Alignment format.
+.HP
+\fB\-R\fR <tag>
+.IP
+Before estimating transition probabilities, group features by <tag>
+(e.g., "transcript_id" or "exon_id") and reverse complement
+segments of the alignment corresponding to groups on the
+reverse strand. Groups must be non\-overlapping (see refeature
+\fB\-\-unique\fR).
+.SS indel options
+.HP
+\fB\-I\fR <indel_cat_list>
+.TP
+Model indels for specified categories.
+To have
+.IP
+nonzero probability for the states corresponding to a
+specified category range, indels must be "clean"
+(nonoverlapping), must be assignable by parsimony to a single
+branch in the phylogenetic tree, and must have lengths that
+are exact multiples of the category range size. Avoid \fB\-G\fR with
+this option. If used in training mode, requires \fB\-T\fR.
+.HP
+\fB\-t\fR <tree_fname>
+.IP
+Use the specified tree topology when training
+for indels.
+.HP
+\fB\-n\fR <nseqs>
+.IP
+Train an indel model for <nseqs>
+sequences, despite that the training alignment has a different
+number. All (non\-trivial) gap patterns are assumed to be
+equally frequent.
+.SS other options
+.HP
+\fB\-q\fR
+.IP
+Proceed quietly (without updates to stderr).
+.HP
+\fB\-h\fR
+.IP
+Print this help message and exit.
diff --git a/debian/help2man/hmm_tweak.1 b/debian/help2man/hmm_tweak.1
new file mode 100644
index 0000000..aa23bdd
--- /dev/null
+++ b/debian/help2man/hmm_tweak.1
@@ -0,0 +1,59 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH HMM_TWEAK "1" "May 2016" "hmm_tweak 1.4" "User Commands"
+.SH NAME
+hmm_tweak \- Alter transition probabilities in an HMM definition file.
+.SH DESCRIPTION
+Alter transition probabilities in an HMM definition file.
+After specified operations are performed, transition
+probabilities are renormalized and the adjusted file is
+written to standard out. This program may be used
+multiple times in a pipe.
+.SH USAGE
+hmm_tweak [OPTIONS] <file.hmm> <cmap.cm>
+.SH OPTIONS
+.TP
+\fB\-f\fR <cats>
+Operate on transitions *from* states corresponding to the
+specified category names (default all)
+\fB\-t\fR <cats>
+Operate on transitions *to* states corresponding to the
+specified category names (default all)
+\fB\-m\fR <fact>
+Multiply transition probabilities by the specified factor.
+.HP
+\fB\-a\fR <const> Add the specified constant to transition probabilities.
+\fB\-e\fR <val>
+Set transition probabilities equal to the specified value.
+.HP
+\fB\-i\fR <icats> Assume a phylo\-HMM indel model for states corresponding to
+.IP
+the specified category names.
+\fB\-u\fR <tree>
+(Required with \fB\-i\fR) Assume given tree topology (.nh file).
+\fB\-F\fR <gps>
+(For use with \fB\-i\fR) Operate on transitions from states corresp.
+to the specified gap\-pattern numbers (ANDed with \fB\-f\fR).
+.TP
+\fB\-T\fR <gps>
+(For use with \fB\-i\fR) Operate on transitions to states corresp.
+to the specified gap\-pattern numbers (ANDed with \fB\-t\fR).
+\fB\-z\fR
+Equalize transition probabilities. Set all transition
+probabilities indicated by \fB\-f\fR/\-t/\-F/\-T to their overall
+average value. Options \fB\-m\fR and/or \fB\-a\fR can be used to adjust
+this average value.
+\fB\-R\fR
+Restrict to successive transitions within a category range.
+\fB\-y\fR
+Like \fB\-z\fR, except compute separate averages for five classes
+of transitions, based on the gap patterns of the states
+involved: between null gap patterns, between equal
+non\-null gap patterns, from null to non\-null gap
+patterns, from non\-null to null gap patterns, and all
+others. Useful with the indel model when training data
+is sparse (e.g., for splice\-site states). Options \fB\-m\fR and \fB\-a\fR
+will be applied to transitions of the 3rd and 5th classes
+described.
+.TP
+\fB\-h\fR
+Print this help message.
diff --git a/debian/help2man/hmm_view.1 b/debian/help2man/hmm_view.1
new file mode 100644
index 0000000..e3a3129
--- /dev/null
+++ b/debian/help2man/hmm_view.1
@@ -0,0 +1,33 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH HMM_VIEW "1" "May 2016" "hmm_view 1.4" "User Commands"
+.SH NAME
+hmm_view \- produces a graphical description of the state-transition
+.SH DESCRIPTION
+produces a graphical description of the state\-transition
+structure of a phylo\-HMM, which can be converted to a viewable image
+using the 'dot' program. (http://www.graphviz.org)
+.SH SYNOPSIS
+hmm_view [OPTIONS] <hmm_fname> <cat_map_fname>|<cat_map_str>
+.SH OPTIONS
+.TP
+\fB\-k\fR <nrcats>
+Assume a separate version of each state for each of
+<nrcats> rate categories.
+.TP
+\fB\-i\fR <icats>
+Assume use of indel model for specified category names.
+.TP
+\fB\-t\fR <tree>
+(Required with \fB\-i\fR) Tree topology to assume for indel
+model (.nh file).
+.TP
+\fB\-C\fR <cats>
+Show only the states corresponding to the specified
+category names.
+.TP
+\fB\-R\fR <piv>
+Reflect the HMM about the specified 'pivot' categories.
+(Not yet implemented.)
+.TP
+\fB\-x\fR
+Don't show unconnected states.
diff --git a/debian/help2man/indelFit.1 b/debian/help2man/indelFit.1
new file mode 100644
index 0000000..903a39d
--- /dev/null
+++ b/debian/help2man/indelFit.1
@@ -0,0 +1,55 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH INDELFIT "1" "May 2016" "indelFit 1.4" "User Commands"
+.SH NAME
+indelFit \- Estimate the parameters of a simple indel model, given an indel history
+.SH DESCRIPTION
+Estimate the parameters of a simple indel model, given an indel history
+and a tree. By default, writes estimates of three parameters to
+stdout: an insertion rate alpha, a deletion rate beta, and a parameter
+tau roughly equal to the inverse of the expected indel length (modulo
+adjustments required to make probabilities sum to one).
+.IP
+An indel history can be obtained with indelHistory and a tree with
+phyloFit.
+.SH OPTIONS
+.HP
+\fB\-\-alpha\fR, \fB\-a\fR <val>
+.TP
+Starting value of alpha, the insertion rate.
+Default is 0.02.
+.HP
+\fB\-\-beta\fR, \fB\-b\fR <val>
+Starting value of beta, the deletion rate.
+Default is 0.04.
+.HP
+\fB\-\-tau\fR, \fB\-t\fR <val>
+Starting value of tau, the length parameter.
+Default is 0.05.
+.HP
+\fB\-\-lnl\fR, \fB\-L\fR
+.IP
+Compute log likelihood of model only, without optimizing parameters.
+The options above can be used to set the parameters as desired.
+.HP
+\fB\-\-columns\fR, \fB\-c\fR
+.IP
+Output log likelihood of each column.
+.HP
+\fB\-\-features\fR, \fB\-f\fR <file.gff>
+.IP
+Estimate separate parameters for each type of feature in the given
+file, as well as for background sites.
+.HP
+\fB\-\-reference\fR, \fB\-r\fR <name>
+.IP
+(For use with \fB\-\-features\fR) Name of species (node of tree) defining
+coordinate frame of features. By default, the coordinate frame of
+the entire alignment is assumed.
+.HP
+\fB\-\-log\fR, \fB\-l\fR <file>
+.IP
+Write log of optimization to specified file.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Display this help message and exit.
diff --git a/debian/help2man/indelHistory.1 b/debian/help2man/indelHistory.1
new file mode 100644
index 0000000..e4d12cc
--- /dev/null
+++ b/debian/help2man/indelHistory.1
@@ -0,0 +1,43 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH INDELHISTORY "1" "May 2016" "indelHistory 1.4" "User Commands"
+.SH NAME
+indelHistory \- Obtain an "indel history" for an alignment and write it to a file
+.SH DESCRIPTION
+Obtain an "indel history" for an alignment and write it to a file
+describing insertions and deletions in all species using a compact
+format. The specified alignment may either contain sequences
+corresponding only to leaves of the specified tree, in which case an
+indel history will be inferred using a simple parsimony algorithm, or
+it may contain sequences for all nodes in the tree, in which case the
+indel history will simply be extracted from the file.
+.SH OPTIONS
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|MAF|SS|....
+.IP
+Read alignment in specified file format (default FASTA).
+.HP
+\fB\-\-output\-alignment\fR, \fB\-A\fR
+.IP
+Instead of a summary of indels only, output an alignment in FASTA
+format of sequences for all ancestral and leaf nodes.
+.HP
+\fB\-\-read\-history\fR, \fB\-H\fR <fname>
+Read an indel history directly from the specified file.
+Useful for
+debugging.
+The alignment and tree arguments are not required;
+.IP
+however in an alignment is given with \fB\-\-read\-history\fR and
+\fB\-\-output\-alignment\fR, then actual bases can be output for leaf
+species.
+.HP
+\fB\-\-ia\-names\fR, \fB\-I\fR
+.IP
+Assume ancestral sequences in alignment.fa are named according to
+the convention used by Mathieu Blanchette's inferAncestors program,
+e.g., "RAT+MOUSE+RABBIT+" for the last common ancestor of "rat",
+"mouse", and "rabbit".
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Display this help message.
diff --git a/debian/help2man/maf_parse.1 b/debian/help2man/maf_parse.1
new file mode 100644
index 0000000..84b82f5
--- /dev/null
+++ b/debian/help2man/maf_parse.1
@@ -0,0 +1,172 @@
+.TH MAF_PARSE "1" "May 2016" "maf_parse 1.4" "User Commands"
+.SH NAME
+maf_parse \- Reads a MAF file and perform various operations on it.
+.SH DESCRIPTION
+Reads a MAF file and perform various operations on it.
+Performs parsing operations block\-by\-block whenever possible,
+rather than storing entire alignment in memory.
+Can extract a sub\-alignment from an alignment (by row
+or by column).
+Can extract features given GFF, BED, or
+genepred file.
+Can also extract sub\-features such as CDS1,2,3
+or 4d sites.
+Can perform various functions such as gap
+stripping or re\-ordering of sequences.
+Capable of reading and
+.IP
+writing in a few common formats, but will not load input or output
+alignments into memory if output format is MAF.
+.SH OPTIONS
+.SS Output format
+.HP
+\fB\-\-out\-format\fR, \fB\-o\fR MAF|PHYLIP|FASTA|MPM|SS
+(Default MAF).
+Output file format. SS format is only
+available un\-ordered.
+Note that some options, which involve
+reversing alignments based on strand, or stripping gaps,
+cannot be output in MAF format and use FASTA by default.
+Also note that when output format is not MAF, the entire
+output must be loaded into memory.
+.HP
+\fB\-\-pretty\fR, \fB\-p\fR
+.IP
+Pretty\-print alignment (use '.' when character matches
+corresponding character in first sequence). Ignored if
+\fB\-\-out\-format\fR SS is selected.
+.SS Obtaining sub\-alignments and re\-ordering rows
+.HP
+\fB\-\-start\fR, \fB\-s\fR <start_col>
+Start index of sub\-alignment (indexing starts with 1).
+Coordinates are in terms of the reference sequence unless
+the \fB\-\-no\-refseq\fR option is used, in which case they are in
+terms of alignment columns. Default is 1.
+.HP
+\fB\-\-end\fR, \fB\-e\fR <end_col>
+End index of sub\-alignment.
+Default is length of alignment.
+.IP
+Coordinates defined as in \fB\-\-start\fR option, above.
+.HP
+\fB\-\-seqs\fR, \fB\-l\fR <seq_list>
+.IP
+Comma\-separated list of sequences to include (default)
+exclude (if \fB\-\-exclude\fR). Indicate by sequence number or name
+(numbering starts with 1 and is evaluated *after* \fB\-\-order\fR is
+applied).
+.HP
+\fB\-\-exclude\fR, \fB\-x\fR
+Exclude rather than include specified sequences.
+.HP
+\fB\-\-order\fR, \fB\-O\fR <name_list>
+.IP
+Change order of rows in alignment to match sequence names
+specified in name_list. The first name in the alignment becomes
+the reference sequence.
+.HP
+\fB\-\-no\-refseq\fR, \fB\-n\fR
+Do not assume first sequence in MAF is refseq.
+Instead, use
+coordinates
+given by absolute position in alignment (starting
+from 1).
+.SS Splitting into multiple MAFs by length
+.HP
+\fB\-\-split\fR, \fB\-S\fR length
+.IP
+Split MAF into pieces by length, and puts output in
+outRootX.maf, where X=1,2,...,numPieces. outRoot can be
+modified with \fB\-\-out\-root\fR, and the minimum number of digits in X
+can be modified with \fB\-\-out\-root\-digits\fR.
+Splits between blocks, so that each output file does not exceed
+specified length. By default, length is counted by distance
+spanned in alignment by refseq, unless \fB\-\-no\-refseq\fR is specified.
+.HP
+\fB\-\-out\-root\fR, \fB\-r\fR <name>
+.IP
+Filename root for output files produced by \fB\-\-split\fR (default
+"maf_parse").
+.HP
+\fB\-\-out\-root\-digits\fR, \fB\-d\fR <numdigits>
+(for use with \fB\-\-split\fR).
+The minimum number of digits used to
+.IP
+index each output file produced by split.
+.SS Extracting features from MAF
+.HP
+\fB\-\-features\fR, \fB\-g\fR <fname>
+Annotations file.
+May be GFF, BED, or genepred format.
+.IP
+Coordinates assumed to be in frame of first sequence of
+alignment (reference sequence). By default, outputs subset of
+MAF which are labeled in annotations file. But can be used with
+\fB\-\-by\-category\fR, \fB\-\-by\-group\fR, and/or \fB\-\-do\-cats\fR to split MAF by
+annotation type. Or if used with \fB\-\-mask\-features\fR, is only used
+to determine regions to mask. Implies \fB\-\-strip\-i\-lines\fR,
+\fB\-\-strip\-e\-lines\fR
+.HP
+\fB\-\-by\-category\fR, \fB\-L\fR
+.TP
+(Requires \fB\-\-features\fR).
+Split by category, as defined by
+annotations file and (optionally) category map (see \fB\-\-catmap\fR).
+.HP
+\fB\-\-do\-cats\fR, \fB\-C\fR <cat_list>
+(For use with \fB\-\-by\-category\fR) Output sub\-alignments for only the
+specified categories.
+.HP
+\fB\-\-catmap\fR, \fB\-c\fR <fname>|<string>
+.IP
+(Optionally use with \fB\-\-by\-category\fR) Mapping of feature types to
+category numbers. Can either give a filename or an "inline"
+description of a simple category map, e.g.,
+.HP
+\fB\-\-catmap\fR "NCATS = 3 ; CDS 1\-3" or
+.HP
+\fB\-\-catmap\fR "NCATS = 1; UTR 1".
+.HP
+\fB\-\-by\-group\fR, \fB\-P\fR <tag>
+(Requires \fB\-\-features\fR).
+Split by groups in annotation file, as
+defined by specified tag.
+.SS Masking by quality score
+.HP
+\fB\-\-mask\-bases\fR, \fB\-b\fR <qscore>
+Mask all bases with quality score <= n.
+Note that n is in the
+same units as displayed in the MAF (ranging from 0\-9), and
+represents min(9, floor(PHRED_score/5)). Bases without any
+quality score will not be masked.
+.HP
+\fB\-\-masked\-file\fR, \fB\-m\fR <filename>
+(For use with \fB\-\-mask\-bases\fR).
+Write a file containing all the
+regions masked for low quality.
+The file will be in 0\-based
+coordinates relative to the refseq, with an additional column
+giving the name of the species masked. Note that low\-quality bases
+masked at alignment columns with a gap in the reference sequence
+may not be represented in the output file.
+.HP
+\fB\-\-mask\-features\fR \fB\-M\fR <spec>
+(Requires \fB\-\-features\fR).
+Mask all bases annotated in features in the
+given species (can be a comma\-delimited list of species).
+Note that
+.IP
+coordinates are always in terms of refseq, even if a different species
+is being masked.
+.SS Other
+.HP
+\fB\-\-strip\-i\-lines\fR, \fB\-I\fR
+.IP
+Remove lines in MAF starting with i.
+.HP
+\fB\-\-strip\-e\-lines\fR, \fB\-E\fR
+Remove lines in MAF starting with e.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
diff --git a/debian/help2man/makeHKY.1 b/debian/help2man/makeHKY.1
new file mode 100644
index 0000000..7d9413e
--- /dev/null
+++ b/debian/help2man/makeHKY.1
@@ -0,0 +1,32 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH MAKEHKY "1" "May 2016" "makeHKY 1.4" "User Commands"
+.SH NAME
+makeHKY \- Generates an HKY tree model, given kappa (the transition/transversion
+.SH DESCRIPTION
+Generates an HKY tree model, given kappa (the transition/transversion
+rate ratio). The equilibrium base composition and either a branch
+length or a complete tree can be specified by the options described
+below.
+.SH OPTIONS
+.HP
+\fB\-\-gc\fR, \fB\-g\fR <val>
+.IP
+Define base composition according to specified G+C composition,
+assuming P(A)=P(T) and P(C)=P(G). Default is 0.4.
+.HP
+\fB\-\-pi\fR, \fB\-p\fR <pi_A,pi_C,pi_G,pi_T>
+Override \fB\-\-gc\fR and define base composition explicitly.
+Values will
+be renormalized to ensure they sum exactly to one.
+.HP
+\fB\-\-branch\-length\fR, \fB\-t\fR <val>
+.IP
+Assume a tree consisting of a single branch of specified length.
+Default value is 1.
+.HP
+\fB\-\-tree\fR, \fB\-T\fR <tree.nh>
+Override \fB\-\-branch\-length\fR and use specified tree.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Display this help message and exit.
diff --git a/debian/help2man/modFreqs.1 b/debian/help2man/modFreqs.1
new file mode 100644
index 0000000..13948bd
--- /dev/null
+++ b/debian/help2man/modFreqs.1
@@ -0,0 +1,19 @@
+.TH MODFREQS "1" "May 2016" "modFreqs 1.4" "User Commands"
+.SH NAME
+modFreqs \- Change background frequencies of reversible tree model in such
+.SH DESCRIPTION
+Change background frequencies of reversible tree model in such
+a way that reversibility is maintained.
+.SH SYNOPSIS
+.B modFreqs
+tree.mod <Afreq> <Cfreq> <Gfreq> <Tfreq> > new.mod
+.IP
+OR
+.PP
+.B modFreqs
+tree.mod <G+Cfreq> > new.mod
+.SH OPTIONS
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
diff --git a/debian/help2man/msa_diff.1 b/debian/help2man/msa_diff.1
new file mode 100644
index 0000000..2455ac8
--- /dev/null
+++ b/debian/help2man/msa_diff.1
@@ -0,0 +1,31 @@
+.TH MSA_DIFF "1" "May 2016" "msa_diff 1.4" "User Commands"
+.SH NAME
+msa_diff \- Compare two multiple alignments and report differences.
+.SH DESCRIPTION
+Compare two multiple alignments and report differences.
+.SH OPTIONS
+.HP
+\fB\-\-format1\fR, \fB\-i\fR FASTA|SS|PHYLIP|MPM|MAF
+.IP
+Format of first alignment (default is to guess format from file contents).
+.HP
+\fB\-\-format2\fR, \fB\-j\fR FASTA|SS|PHYLIP|MPM|MAF
+Format of second alignment (default is to guess format from file contents).
+.HP
+\fB\-\-alphabet\fR, \fB\-a\fR <alphabet_string>
+Use given string for alphabet.
+Can be used to accommodate
+.IP
+nonstandard characters (e.g., 'b' for any base or '^' for insertion
+gaps, '.' for deletion gaps).
+.HP
+\fB\-\-ignore\-base\-id\fR, \fB\-b\fR
+Ignore identity of bases; consider all alphabetical characters
+equivalent (e.g., A, C, G, T, N, X, b).
+.HP
+\fB\-\-ignore\-gap\-type\fR, \fB\-g\fR
+.IP
+Ignore type of gap; consider '\-', '^', and '.' all equivalent.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+Display this help message and exit.
diff --git a/debian/help2man/msa_split.1 b/debian/help2man/msa_split.1
new file mode 100644
index 0000000..31760c5
--- /dev/null
+++ b/debian/help2man/msa_split.1
@@ -0,0 +1,228 @@
+.TH MSA_SPLIT "1" "May 2016" "msa_split 1.4" "User Commands"
+.SH NAME
+msa_split \- Partitions a multiple sequence alignment either at designated
+.SH DESCRIPTION
+Partitions a multiple sequence alignment either at designated
+columns, or according to specified category labels, and outputs
+sub\-alignments for the partitions. Optionally splits an
+associated annotations file.
+.SH EXAMPLE
+.PP
+(See below for details on options)
+.PP
+1. Read an alignment for a whole human chromosome from a MAF file
+and extract sub\-alignments in 1Mb windows overlapping by 1kb. Use
+sufficient statistics (SS) format for output (can be used by
+phyloFit, phastCons, or exoniphy). Set window boundaries between
+alignment blocks, if possible.
+.IP
+msa_split chr1.maf \fB\-\-refseq\fR chr1.fa \fB\-\-in\-format\fR MAF
+\fB\-\-windows\fR 1000000,1000 \fB\-\-out\-format\fR SS
+\fB\-\-between\-blocks\fR 5000 \fB\-\-out\-root\fR chr1
+.PP
+(Windows will be defined using the coordinate system of the first
+sequence in the alignment, assumed to be the reference sequence;
+output will be to chr1.1\-1000000.ss, chr1.999001\-1999000.ss, ...)
+.PP
+2. As in (1), but report unordered sufficient statistics (much
+more compact and adequate for use with phyloFit).
+.IP
+msa_split chr1.maf \fB\-\-refseq\fR chr1.fa \fB\-\-in\-format\fR MAF
+\fB\-\-windows\fR 1000000,1000 \fB\-\-out\-format\fR SS
+\fB\-\-between\-blocks\fR 5000 \fB\-\-out\-root\fR chr1 \fB\-\-unordered\-ss\fR
+.PP
+3. Extract sub\-alignments of sites in conserved elements and not
+in conserved elements, as defined by a BED file (coordinates
+assumed to be for 1st sequence). Read multiple alignment in FASTA
+format.
+.IP
+msa_split mydata.fa \fB\-\-features\fR conserved.bed \fB\-\-by\-category\fR
+\fB\-\-out\-root\fR mydata
+.PP
+(Output will be to mydata.background\-0.fa and mydata.bed_feature\-1.fa
+[latter has sites of category number 1, defined by bed file]
+3. Extract sub\-alignments of sites in each of the three codon
+positions, as defined by a GFF file (coordinates assumed to be for
+1st sequence). Reverse complement genes on minus strand.
+.IP
+msa_split chr22.maf \fB\-\-in\-format\fR MAF \fB\-\-features\fR chr22.gff
+\fB\-\-by\-category\fR \fB\-\-catmap\fR "NCATS 3 ; CDS 1\-3" \fB\-\-do\-cats\fR CDS
+\fB\-\-reverse\-compl\fR \fB\-\-out\-root\fR chr22 \fB\-\-out\-format\fR SS
+.PP
+(Output will be to chr22.cds\-1.ss, chr22.cds\-2.ss, chr22.cds\-3.ss)
+.PP
+4. Split an alignment into pieces corresponding to the genes in a
+GFF file. Assume genes are defined by the tag "transcript_id".
+.IP
+msa_split cftr.fa \fB\-\-features\fR cftr.gff \fB\-\-by\-group\fR transcript_id
+.PP
+5. Obtain a sub\-alignment for each of a set of regulatory regions,
+as defined in a BED file.
+.IP
+msa_split chr22.maf \fB\-\-in\-format\fR MAF \fB\-\-refseq\fR chr22.fa
+\fB\-\-features\fR chr22.reg.bed \fB\-\-for\-features\fR
+\fB\-\-out\-root\fR chr22.reg
+.SH OPTIONS
+.SS Splitting options
+.HP
+\fB\-\-windows\fR, \fB\-w\fR <win_size,win_overlap>
+.IP
+Split the alignment into "windows" of size <win_size> bases,
+overlapping by <win_overlap>.
+.HP
+\fB\-\-by\-category\fR, \fB\-L\fR
+.IP
+(Requires \fB\-\-features\fR) Split by category, as defined by
+annotations file and (optionally) category map (see
+\fB\-\-catmap\fR)
+.HP
+\fB\-\-by\-group\fR, \fB\-P\fR <tag>
+.IP
+(Requires \fB\-\-features\fR) Split by groups in annotation file,
+as defined by specified tag. Splits midway between every
+pair of consecutive groups. Features will be sorted by group.
+There should be no overlapping features (see 'refeature
+\fB\-\-unique\fR').
+.HP
+\fB\-\-for\-features\fR, \fB\-F\fR
+(Requires \fB\-\-features\fR) Extract section of alignment
+corresponding to every feature. There will be no output for
+regions not covered by features.
+.HP
+\fB\-\-by\-index\fR, \fB\-p\fR <indices>
+List of explicit indices at which to split alignment
+(comma\-separated). If the list of indices is "10,20",
+then sub\-alignments will be output for sites 1\-9, 10\-19, and
+20\-<msa_len>. Note that the indices are relative to the
+input alignment, and not necessarily in genomic coordinates.
+.HP
+\fB\-\-npartitions\fR, \fB\-n\fR <number>
+.IP
+Split alignment equally into specified number of partitions.
+.HP
+\fB\-\-between\-blocks\fR, \fB\-B\fR <radius>
+(Not for use with \fB\-\-by\-category\fR or \fB\-\-for\-features\fR) Try to
+partition at sites between alignment blocks. Assumes a
+reference sequence alignment, with the first sequence as the
+reference seq (as created by multiz). Blocks of 30 sites with
+gaps in all sequences but the reference seq are assumed to
+indicate boundaries between alignment blocks. Partition
+indices will not be moved more than <radius> sites.
+.HP
+\fB\-\-features\fR, \fB\-g\fR <fname>
+.IP
+(For use with \fB\-\-by\-category\fR, \fB\-\-by\-group\fR, \fB\-\-for\-features\fR, or
+\fB\-\-windows\fR) Annotations file. May be GFF, BED, or genepred
+format. Coordinates are assumed to be in the coordinate frame of
+the first sequence in the alignment (assumed to be the reference
+sequence).
+.HP
+\fB\-\-catmap\fR, \fB\-c\fR <fname>|<string>
+(Optionally use with \fB\-\-by\-category\fR) Mapping of feature types
+to category numbers. Can either give a filename or an
+"inline" description of a simple category map, e.g.,
+\fB\-\-catmap\fR "NCATS = 3 ; CDS 1\-3" or \fB\-\-catmap\fR "NCATS = 1 ; UTR
+1".
+.HP
+\fB\-\-refidx\fR, \fB\-d\fR <frame_index>
+.IP
+(For use with \fB\-\-windows\fR or \fB\-\-by\-index\fR) Index of frame of
+reference for split indices. Default is 1 (1st sequence
+assumed reference).
+.SH File names & formats, type of output, etc.
+.HP
+\fB\-\-in\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
+Input alignment file format.
+Default is to guess format from
+.IP
+file contents.
+.HP
+\fB\-\-refseq\fR, \fB\-M\fR <fname>
+.IP
+(For use with \fB\-\-in\-format\fR MAF) Name of file containing
+reference sequence, in FASTA format.
+.HP
+\fB\-\-out\-format\fR, \fB\-o\fR FASTA|PHYLIP|MPM|SS
+Output alignment file format.
+Default is FASTA.
+.HP
+\fB\-\-out\-root\fR, \fB\-r\fR <name>
+Filename root for output files (default "msa_split").
+.HP
+\fB\-\-sub\-features\fR, \fB\-f\fR
+(For use with \fB\-\-features\fR)
+Output subsets of features
+corresponding to subalignments.
+Features overlapping
+partition boundaries will be discarded.
+Not permitted with
+.HP
+\fB\-\-by\-category\fR.
+.HP
+\fB\-\-reverse\-compl\fR, \fB\-s\fR
+.IP
+Reverse complement all segments having at least one feature on
+the reverse strand and none on the positive strand. For use
+with \fB\-\-by\-group\fR. Can also be used with \fB\-\-by\-category\fR to ensure
+all sites in a category are represented in the same strand
+orientation.
+.HP
+\fB\-\-gap\-strip\fR, \fB\-G\fR ALL|ANY|<seqno>
+.IP
+Strip columns in output alignments containing all gaps, any
+gaps, or gaps in the specified sequence (<seqno>; indexing
+begins with one). Default is not to strip any columns.
+.HP
+\fB\-\-seqs\fR, \fB\-l\fR <seq_list>
+Include only specified sequences in output.
+Indicate by
+.IP
+sequence number or name (numbering starts with 1 and is
+evaluated *after* \fB\-\-order\fR is applied).
+.HP
+\fB\-\-exclude\fR, \fB\-x\fR
+Exclude rather than include specified sequences.
+.HP
+\fB\-\-order\fR, \fB\-O\fR <name_list>
+.IP
+Change order of rows in alignment to match sequence names
+specified in name_list. If a name appears in name_list but
+not in the alignment, a row of gaps will be inserted.
+.HP
+\fB\-\-min\-informative\fR, \fB\-I\fR <n>
+.IP
+Only output alignments having at least <n> informative sites
+(sites at which at least two non\-gap and non\-N gaps are present).
+.HP
+\fB\-\-do\-cats\fR, \fB\-C\fR <cat_list>
+(For use with \fB\-\-by\-category\fR) Output sub\-alignments for only the
+specified categories (column\-delimited list).
+.HP
+\fB\-\-tuple\-size\fR, \fB\-T\fR <tuple_size>
+.IP
+(for use with \fB\-\-by\-category\fR or \fB\-\-out\-format\fR SS) Size of tuples
+of columns to consider in downstream analysis (e.g., with
+context\-dependent phylogenetic models; see 'phyloFit'). With
+\fB\-\-by\-category\fR, insert tuple_size\-1 columns of missing data
+between sites that were not adjacent in the original alignment,
+to avoid creating artificial context. With \fB\-\-out\-format\fR SS,
+express sufficient statistics in terms of tuples of specified size.
+.HP
+\fB\-\-unordered\-ss\fR, \fB\-z\fR
+(For use with \fB\-\-out\-format\fR SS)
+Suppress the portion of the
+sufficient statistics concerned with the order in which columns
+appear.
+.HP
+\fB\-\-summary\fR, \fB\-S\fR
+.IP
+Output summary of each output alignment to a file with suffix
+".sum" (includes base frequencies and numbers of gapped columns).
+.SS Other
+.HP
+\fB\-\-quiet\fR, \fB\-q\fR
+Proceed quietly.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
diff --git a/debian/help2man/msa_view.1 b/debian/help2man/msa_view.1
new file mode 100644
index 0000000..d8a7d56
--- /dev/null
+++ b/debian/help2man/msa_view.1
@@ -0,0 +1,378 @@
+.TH MSA_VIEW "1" "May 2016" "msa_view 1.4" "User Commands"
+.SH NAME
+msa_view \- Provides various kinds of "views" of one or more multiple
+.SH DESCRIPTION
+Provides various kinds of "views" of one or more multiple
+alignments. Can extract a sub\-alignment from an alignment (by row
+or by column) or combine several alignments into one. Also can
+extract the sufficient statistics for phylogenetic analysis from
+an alignment, optionally accounting for site categories that are
+defined by an auxiliary annotations file. Supports various other
+functions, including gap stripping, column randomization, and
+reordering of sequences. Capable of reading and writing in a few
+common formats. Can be used for file conversion (by default,
+output is the entire input alignment).
+.SH EXAMPLE
+.PP
+(See below for more details on options)
+.PP
+1. Convert alignment formats (default input and output is FASTA)
+.IP
+msa_view myfile.fa \fB\-\-out\-format\fR PHYLIP > myfile.ph
+.IP
+msa_view myfile2.raw \fB\-\-in\-format\fR MPM > myfile2.fa
+.PP
+2. Obtain a sub\-alignment by position, using the coordinate frame
+of the first sequence in the alignment.
+.IP
+msa_view myfile.fa \fB\-\-start\fR 1234 \fB\-\-end\fR 5678 \fB\-\-refidx\fR 1 > mysub.fa
+.PP
+3. Obtain a sub\-alignment by sequence.
+.IP
+msa_view myfile.fa \fB\-\-seqs\fR 1,4,5 > seqs145.fa
+.IP
+msa_view myfile.fa \fB\-\-seqs\fR 1,4,5 \fB\-\-exclude\fR > seqs236.fa
+.PP
+(can also specify sequences by name, e.g., \fB\-\-seqs\fR cow,rat,pig)
+.PP
+4. Concatenate alignments.
+.IP
+msa_view \fB\-\-aggregate\fR human,mouse,rat myf1.fa myf2.fa myf3.fa
+\f(CW> concat.fa\fR
+.PP
+(source alignments may have different subsets of sequences and may
+use different sequence orders; here, human,mouse,rat defines full
+set and order in output alignment)
+.PP
+5. Extract sufficient statistics from a FASTA file.
+.IP
+msa_view myfile.fa \fB\-\-out\-format\fR SS > myfile.ss
+.PP
+6. Extract sufficient statistics from a MAF file for a complete
+human chromosome. (Can be used by phyloFit.)
+.IP
+msa_view chr1.maf \fB\-\-out\-format\fR SS > chr1.ss
+.PP
+7. As in (6), but include information about regions of the
+reference sequence not present in the MAF file, and include a
+representation of the order in which alignment columns occur
+(needed by programs such as phastCons or exoniphy).
+.IP
+msa_view chr1.maf \fB\-\-refseq\fR chr1.fa
+\fB\-\-out\-format\fR SS > chr1.ordered.ss
+.PP
+8. As in (6), but collect statistics for pairs of adjacent sites
+(can be used by phyloFit to estimate a dinucleotide model).
+.IP
+msa_view chr1.maf \fB\-\-out\-format\fR SS
+\fB\-\-tuple\-size\fR 2 > chr1.pairs.ss
+.PP
+9. Pool sufficient statistics from several human chromosomes.
+.IP
+msa_view \fB\-\-aggregate\fR human,mouse,rat
+\fB\-\-out\-format\fR SS chr1.ss chr2.ss chr3.ss > chr123.ss
+.PP
+10. Extract separate sufficient statistics for the three codon
+positions, as defined by annotations in a GFF file.
+.IP
+msa_view chr1.maf \fB\-\-features\fR chr22.gff
+\fB\-\-catmap\fR "NCATS = 3; CDS 1\-3" \fB\-\-out\-format\fR SS
+> chr22.pos.ss
+.PP
+11. As in (10), but re\-orient genes on \- strand so that stats
+reflect + strand. Assume genes are defined by tag "transcript_id".
+.IP
+msa_view chr1.maf \fB\-\-features\fR chr22.gff
+\fB\-\-catmap\fR "NCATS = 3; CDS 1\-3" \fB\-\-reverse\-groups\fR transcript_id
+\fB\-\-out\-format\fR SS > chr22.pos.ss
+.SH OPTIONS
+.SS Obtaining sub\-alignments and combining alignments
+.HP
+\fB\-\-start\fR, \fB\-s\fR <start_col>
+.IP
+Starting column of sub\-alignment (indexing starts with 1).
+Default is 1. Note that coordinates use the frame of reference
+of the entire alignment unless \fB\-\-refidx\fR 1 is specified.
+.HP
+\fB\-\-end\fR, \fB\-e\fR <end_col>
+.TP
+Ending column of sub\-alignment.
+Default is length of
+.TP
+alignment.
+Note that coordinates use the frame of reference
+.IP
+of the entire alignment unless \fB\-\-refidx\fR 1 is specified.
+.HP
+\fB\-\-seqs\fR, \fB\-l\fR <seq_list>
+Comma\-separated list of sequences to include (default)
+exclude (if \fB\-\-exclude\fR). Indicate by sequence number or name
+(numbering starts with 1 and is evaluated *after* \fB\-\-order\fR is
+applied).
+.HP
+\fB\-\-exclude\fR, \fB\-x\fR
+.IP
+Exclude rather than include specified sequences.
+.HP
+\fB\-\-refidx\fR, \fB\-r\fR <ref_seq>
+.TP
+Index of reference sequence for coordinates.
+Use 0 to
+.IP
+indicate the coordinate system of the alignment as a whole
+(this is the default).
+.HP
+\fB\-\-aggregate\fR, \fB\-A\fR <name_list>
+.IP
+(Not compatible with \fB\-\-start\fR or \fB\-\-end\fR) Create an aggregate
+alignment from a set of alignment files, by concatenating
+individual alignments. If used with \fB\-\-out\-format\fR SS and
+\fB\-\-unordered\-ss\fR, the aggregate alignment will never be created
+explicitly (recommended for large data sets). The argument
+<name_list> must be a list of sequence names, including all
+names in all specified alignments (missing sequences will be
+replaced by rows of missing data). The standard <msa_fname>
+argument should be replaced with a list of (whitespaceseparated) file names.
+.HP
+\fB\-\-split\-all\fR, \fB\-X\fR <filename root>
+.IP
+Split output alignment into separate fasta files by species.
+File naming convention is filename_root.species.fa. If used with
+\fB\-\-gap\-strip\fR, gap characters will be stripped from all output files.
+In this case, '\-\-gap\-strip <s>' should NOT be used (ALL or ANY
+should both work fine).
+.SS File formats, gap stripping, reordering, etc.
+.HP
+\fB\-\-in\-format\fR, \fB\-i\fR PHYLIP|FASTA|MPM|MAF|SS
+.TP
+(Default is to guess format from file contents).
+Input file
+.TP
+format.
+FASTA is as usual. PHYLIP is compatible with the formats
+.TP
+used in the PHYLIP and PAML packages.
+MPM is the format used by the
+.IP
+MultiPipMaker aligner and some other of Webb Miller's older tools.
+MAF ("Multiple Alignment Format") is used by MULTIZ/TBA and the
+UCSC Genome Browser. SS is a simple format describing the
+sufficient statistics for phylogenetic inference (distinct columns
+or tuple of columns and their counts). Use \fB\-\-out\-format\fR SS with
+\fB\-\-in\-format\fR MAF for best efficiency (explicit alignment is
+never created). Also, use \fB\-\-unordered\-ss\fR if possible.
+.HP
+\fB\-\-out\-format\fR, \fB\-o\fR PHYLIP|FASTA|MPM|SS
+(Default FASTA)
+Output file format.
+.HP
+\fB\-\-alphabet\fR, \fB\-a\fR <alphabet_string>
+.TP
+Use the specified alphabet (default "ACGT").
+In addition,
+.IP
+\&'\-' characters are assumed to represent alignment gaps, and
+\&'*' and 'N' characters are allowed for missing data.
+Alphabetical letters not in the alphabet will be converted to
+\&'N's upon input. This option is ignored with SS input (alphabet
+specified within SS files.)
+.HP
+\fB\-\-soft\-masked\fR, \fB\-f\fR
+.IP
+Implies \fB\-\-alphabet\fR 'ACGTNacgtn', useful for soft\-masked sequences.
+.HP
+\fB\-\-unmask\fR, \fB\-u\fR
+.IP
+Remove soft\-masking; convert to uppercase.
+.HP
+\fB\-\-pretty\fR, \fB\-P\fR
+Pretty\-print alignment (use '.' when character matches
+corresponding character in first sequence). Ignored if
+\fB\-\-out\-format\fR SS is selected.
+.HP
+\fB\-\-gap\-strip\fR, \fB\-G\fR ALL|ANY|<s>
+Strip columns containing all gaps, any gaps, or a gap in the
+specified sequence (<s>). Indexing starts at one and refers
+to the list *after* any sequences have been added or
+subtracted (via \fB\-\-seqs\fR and \fB\-\-exclude\fR or \fB\-\-order\fR).
+.HP
+\fB\-\-collapse\-missing\fR, \fB\-p\fR
+.IP
+(For use with \fB\-o\fR SS) Convert all missing\-data characters and
+gaps to "*" characters. Can be used to make sufficient
+statistics more compact, which can improve the performance of
+phyloFit (all missing data and gap characters are typically
+treated the same by phyloFit anyway).
+.HP
+\fB\-\-mark\-missing\fR, \fB\-K\fR <maxlen>
+Convert all gaps of length greater than <maxlen> to "*"
+characters. If \fB\-\-refidx\fR is specified (with a positive index),
+gaps in the designated reference sequence will not be altered.
+This is a useful heuristic for distinguishing between
+microindels and regions of missing data (e.g., due to
+large\-scale indels, incomplete assemblies, or highly
+diverged sequences).
+.HP
+\fB\-\-missing\-as\-indels\fR, \fB\-m\fR
+.IP
+Convert all missing data characters (Ns and *s) to gap
+characters, except for Ns in a reference sequence specified by
+\fB\-\-refidx\fR, which will be replaced by randomly selected
+nucleotides. (This allows the coordinate frame for the
+reference sequence to be maintained; this option is only
+recommended if such Ns are rare.) If \fB\-\-refidx\fR is not
+used, all Ns will be replaced by gaps. You may want to use
+\fB\-\-gap\-strip\fR ALL with this option.
+.HP
+\fB\-\-order\fR, \fB\-O\fR <name_list>
+Change order of rows in alignment to match sequence names
+specified in name_list. If a name appears in name_list but
+not in the alignment, a row of gaps will be inserted. This
+option is applied to the alignment *before* \fB\-\-seqs\fR,
+\fB\-\-refidx\fR, and \fB\-\-gap\-strip\fR are applied.
+.HP
+\fB\-\-reverse\-complement\fR, \fB\-V\fR
+.IP
+Reverse complement output alignment.
+.HP
+\fB\-\-randomize\fR, \fB\-R\fR
+Randomly permute the columns of the source alignment (done
+*before* taking sub\-alignment). Requires an ordered
+representation of the alignment (careful using with
+\fB\-\-in\-format\fR SS|MAF \fB\-\-\fR will create full alignment from
+sufficient statistics).
+.HP
+\fB\-\-fill\-Ns\fR, \fB\-N\fR <s:b\-e>
+.IP
+Fill sequence no. <s> with Ns, from <b> to <e>. Applied before
+\fB\-\-start\fR, \fB\-\-end\fR, \fB\-\-seqs\fR, \fB\-\-gap\-strip\fR, but after \fB\-\-order\fR.
+Coordinate frame depends on \fB\-\-refidx\fR. Can be used
+multiple times.
+.HP
+\fB\-\-summary\-only\fR \fB\-S\fR
+Report only summary statistics, rather than complete
+alignment. Statistics are for alignment that would otherwise
+be output (i.e., after other options have been applied).
+.HP
+\fB\-\-window\-summary\fR, \fB\-w\fR <win_size>
+Like \fB\-S\fR, but output summary statistics for non\-overlapping
+windows of the specified size.
+(Sufficient statistics)
+.HP
+\fB\-\-tuple\-size\fR, \fB\-T\fR <tup_size>
+(For use with \fB\-\-out\-format\fR SS).
+Represent an alignment in
+terms of tuples of columns of the designated size.
+Useful
+.IP
+with context\-dependent phylogenetic models.
+.HP
+\fB\-\-unordered\-ss\fR, \fB\-z\fR
+.TP
+(For use with \fB\-\-out\-format\fR SS).
+Suppress the portion of the
+.IP
+sufficient statistics concerned with the order in which
+columns appear. Useful for analyses for which order is
+unimportant.
+(MAF input)
+.HP
+\fB\-\-refseq\fR, \fB\-M\fR <fname>
+.IP
+Read the complete text of the reference sequence from
+<fname> (FASTA format) and combine it with the contents of
+the MAF file to produce a complete, ordered representation of
+the alignment (unaligned regions will be represented by gaps).
+Best used with \fB\-\-out\-format\fR SS. The reference sequence of the
+MAF file is assumed to be the one that appears first in each
+block.
+.HP
+\fB\-\-keep\-overlapping\fR, \fB\-k\fR
+.IP
+Keep blocks in MAF that have overlapping coordinates in the
+reference (1st) sequence (by default, only the first one is
+kept). Useful in extracting unordered stats from a jumbled
+collection of MAF blocks (e.g., output of Jim Kent's mafFrags
+program).
+Cannot be used with \fB\-\-refseq\fR, \fB\-\-features\fR, or
+.HP
+\fB\-\-cats\-cycle\fR.
+(Site categories: all options require \fB\-\-out\-format\fR SS)
+.HP
+\fB\-\-features\fR, \fB\-g\fR <gff_fname>
+.IP
+(Requires \fB\-\-catmap\fR) Read sequence annotations from the
+specified file (GFF) and label the columns of the alignment
+accordingly. Note: UCSC BED and genepred formats are now
+recognized as well.
+.HP
+\fB\-\-catmap\fR, \fB\-c\fR <fname>|<string>
+.IP
+(optionally use with \fB\-\-features\fR) Mapping of feature types to
+category numbers. Can either give a filename or an "inline"
+description of a simple category map, e.g., \fB\-\-catmap\fR "NCATS =
+3 ; CDS 1\-3" or \fB\-\-catmap\fR "NCATS = 1 ; UTR 1".
+.HP
+\fB\-\-cats\-cycle\fR, \fB\-Y\fR <cycle_size>
+(alternative to \fB\-\-features\fR and \fB\-\-catmap\fR) Assign site categories in
+cycles of the specified size, e.g., as 1,2,3,...,1,2,3 (for
+cycle_size == 3). Useful for in\-frame coding sequence, or to
+partition a data set into nonoverlapping tuples of columns
+(use with \fB\-\-do\-cats\fR).
+.HP
+\fB\-\-do\-cats\fR, \fB\-C\fR <cat_list>
+.TP
+(For use with \fB\-\-features\fR or \fB\-\-cats\-cycle\fR)
+Obtain
+.IP
+sufficient statistics only for the specified categories
+(comma\-delimited list, by number).
+.HP
+\fB\-\-codons\fR, \fB\-D\fR
+Extract sufficient statistics for in\-frame codons.
+Implies
+\fB\-\-tuple\-size\fR 3 \fB\-\-cats\-cycle\fR 3 \fB\-\-do\-cats\fR 3.
+Not appropriate
+.IP
+for use with \fB\-\-features\fR/\-\-catmap.
+.HP
+\fB\-\-reverse\-groups\fR, \fB\-W\fR <tag>
+.IP
+(For use with \fB\-\-features\fR) Group features by <tag> (e.g.,
+"transcript_id" or "exon_id") and reverse complement
+segments of the alignment corresponding to groups on the
+reverse strand. Groups must be non\-overlapping (see refeature
+\fB\-\-unique\fR). Useful when extracting sufficient statistics for
+strand\-specific site categories (e.g., codon positions).
+.HP
+\fB\-\-4d\fR, \fB\-4\fR
+.IP
+(For use with \fB\-\-features\fR; assumes coding regions have feature
+type 'CDS') Extract sufficient statistics for fourfold
+degenerate synonymous sites. Implies \fB\-\-out\-format\fR SS
+\fB\-\-unordered\-stats\fR \fB\-\-tuple\-size\fR 3 \fB\-\-reverse\-groups\fR transcript_id.
+.SH Alignment cleaning
+.HP
+\fB\-\-clean\-coding\fR, \fB\-L\fR <seqname>
+.IP
+Clean an alignment of coding sequences with respect to a named
+reference sequence. Removes sites with gaps and blocks of
+gapless sites smaller than 10 codons in length, ensures
+everything is in\-frame wrt reference sequence, prohibits
+in\-frame stop codons. Reference sequence must begin with a
+start codon and end with a stop codon.
+.HP
+\fB\-\-clean\-indels\fR, \fB\-I\fR <nseqs>
+.TP
+Clean an alignment with special attention to indels.
+Sites
+.IP
+with fewer than <nseqs> bases are removed; bases adjacent to
+indels, and short gapless subsequences, are replaced with Ns.
+If used with \fB\-\-tuple\-size\fR, then <tup_size>\-1 columns of Ns
+will be retained between columns not adjacent in the original
+alignment. Frame is not considered.
+.SS Other
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+Print this help message.
diff --git a/debian/help2man/pbsDecode.1 b/debian/help2man/pbsDecode.1
new file mode 100644
index 0000000..1a0ddd1
--- /dev/null
+++ b/debian/help2man/pbsDecode.1
@@ -0,0 +1,37 @@
+.TH PBSDECODE "1" "May 2016" "pbsDecode 1.4" "User Commands"
+.SH NAME
+pbsDecode \- Decode a binary encoding of a probabilistic biological sequence
+.SH DESCRIPTION
+Decode a binary encoding of a probabilistic biological sequence
+(PBS). Outputs a table with a row for each position in the
+sequence and a column for each base, such that the (i,j)th value
+is the probability of base j at position i. The same codefile
+that was used to encode the sequence should be given.
+.IP
+This program performs the inverse function of pbsEncode.
+.SH EXAMPLE
+Decode an encoded ancestral sequence:
+.IP
+pbsDecode anc.human\-mouse.bin mammal.code > anc.human\-mouse.probs
+.PP
+where "anc.human\-mouse.bin" is a binary encoding of an ancestral
+sequence produced by pbsEncode or prequel, and "mammal.code" is a
+codefile produced by pbsTrain.
+.SH OPTIONS
+.HP
+\fB\-\-start\fR, \fB\-s\fR <sidx>
+.IP
+Decode only the subsequence starting at position <sidx>.
+Indexing starts with 1.
+.HP
+\fB\-\-end\fR, \fB\-e\fR <eidx>
+.IP
+Decode only the subsequence ending at position <eidx>.
+Indexing starts with 1.
+.HP
+\fB\-\-discard\-gaps\fR, \fB\-G\fR
+Do not report gaps in the PBS.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Produce this help message.
diff --git a/debian/help2man/pbsEncode.1 b/debian/help2man/pbsEncode.1
new file mode 100644
index 0000000..0d5d53b
--- /dev/null
+++ b/debian/help2man/pbsEncode.1
@@ -0,0 +1,30 @@
+.TH PBSENCODE "1" "May 2016" "pbsEncode 1.4" "User Commands"
+.SH NAME
+pbsEncode \- Produce an approximate binary encoding of a probabilistic
+.SH DESCRIPTION
+Produce an approximate binary encoding of a probabilistic
+biological sequence (PBS), as defined by a text file
+("input.probs") with a row for each position in the sequence and a
+column for each base. The (i,j)th value in this table should be
+the probability of base j at position i. Columns should be
+white\-space delimited. The encoding will be as defined by
+"codefile", which should be in the format used by pbsTrain.
+.PP
+This program performs the inverse function of pbsDecode.
+.SH EXAMPLE
+.PP
+Encode the probabilities in a file "anc.human\-mouse.probs",
+produced by prequel, using a code file "mammals.code", produced by
+pbsTrain.
+pbsEncode anc.human\-mouse.probs mammals.code > anc.human\-mouse.bin
+.SH OPTIONS
+.HP
+\fB\-\-discard\-gaps\fR, \fB\-G\fR
+.TP
+Discard gaps in the PBS.
+Gaps in the input data are assumed
+.IP
+to be represented by rows consisting of a single "\-" character.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+Produce this help message.
diff --git a/debian/help2man/pbsScoreMatrix.1 b/debian/help2man/pbsScoreMatrix.1
new file mode 100644
index 0000000..bc71318
--- /dev/null
+++ b/debian/help2man/pbsScoreMatrix.1
@@ -0,0 +1,106 @@
+.TH PBSSCOREMATRIX "1" "May 2016" "pbsScoreMatrix 1.4" "User Commands"
+.SH NAME
+pbsScoreMatrix \- Generate log-odds score matrices for use in alignment of
+.SH DESCRIPTION
+Generate log\-odds score matrices for use in alignment of
+probabilistic biological sequences (PBSs). By default, generates
+a matrix for every branch of the tree (as defined in tree.mod),
+but can also generate a matrix for a given branch length (see
+\fB\-\-branch\-length\fR). For a code size of N, an N x N matrix is
+generated by default; \fB\-\-half\-pbs\fR will produce an N x 4 matrix, and
+\fB\-\-no\-pbs\fR will produce a 4 x 4 matrix (assuming a four\-character
+nucleotide alphabet).
+.PP
+Two sequences are assumed to have evolved from a common ancestor
+by a reversible continuous\-time Markov substitution process, and
+to be separated by a branch of length t. The conditional
+probability of a base j in one sequence given a base i in the
+other, P(j | i, t) is given by element (i, j) of the matrix
+.IP
+P(t) = exp(Qt)
+.PP
+where Q is the rate matrix defining the substitution process, and
+element (i, j) of Q is the instantaneous rate at which base i
+changes to base j.
+.PP
+Let S_t(i, j) be a log odds score for the alignment of two bases, i
+and j, based on P(t):
+.IP
+S_t(i, j) = log P(i, j | t) / (pi(i) * pi(j))
+.IP
+= log P(j | i, t) pi(i) / (pi(i) * pi(j))
+.IP
+= log P(j | i, t) / pi(j) (1)
+.PP
+where pi(x) is the "equilibrium" or "background" probability of
+base x. Because of reversibility, S(i, j) = S(j, i), and the S(i,
+j) form a symmetric 4 x 4 matrix. This is the matrix that is
+generated by pbsScoreMatrix with the \fB\-\-no\-pbs\fR option.
+If each "letter" in each sequence represents a probability
+distribution over bases, as in a PBS, then the score for two
+letters k and l can be shown to be
+.IP
+S'_t(k, l) = log sum_i sum_j p_k(i) p_l(j) exp S_t(i, j)
+(2)
+.PP
+where the two sums are over the four bases, p_k(i) is the probability
+of base i under the distribution for k, and p_l(j) is the
+probability of base j under the distribution for l.
+.PP
+Notice that (2) reduces to (1) when p_k(i) = p_l(j) = 1 for some i
+and j and for all other i' and j' p_k(i') = p_l(j') = 0 (i.e.,
+when all of the probability mass is on a single base in both
+distributions and the PBS reduces to an ordinary nucleotide
+sequence). The special case of p_l(j) = 1 only is also of
+interest when aligning a PBS and a nucleotide sequence:
+.IP
+S''_t(k, j) = log sum_i p_k(i) exp S_t(i, j)
+(3)
+.PP
+This is the matrix generated by pbsScoreMatrix with the
+\fB\-\-half\-pbs\fR option.
+Note: all logs are base 2.
+.SH EXAMPLE
+Generate an N x N matrix for every branch of the tree, using a
+code file "code" (generated by pbsTrain) and a tree model file
+"mytree.mod" (generated by phyloFit):
+.IP
+pbsScoreMatrix mytree.mod code > matrices.dat
+.PP
+Generate an N x N matrix for a branch length of 0.2 expected
+substitutions per site.
+.IP
+pbsScoreMatrix \fB\-\-branch\-length\fR 0.2 mytree.mod code > matrix.dat
+.PP
+Generate an N x 4 matrix:
+.IP
+pbsScoreMatrix \fB\-\-branch\-length\fR 0.2 \fB\-\-half\-pbs\fR mytree.mod
+code > matrix.dat
+.PP
+Generate a 4 x 4 matrix:
+.IP
+pbsScoreMatrix \fB\-\-branch\-length\fR 0.2 \fB\-\-no\-pbs\fR code mytree.mod
+\f(CW> matrix.dat\fR
+.PP
+(In this case, a code file is not needed.)
+.SH OPTIONS
+.HP
+\fB\-\-branch\-length\fR, \fB\-t\fR <length>
+.IP
+Output a matrix for a branch of the specified length, rather
+than a matrix for every branch of the tree. The given length
+must be non\-negative and in units of expected substitutions
+per site.
+.HP
+\fB\-\-half\-pbs\fR, \fB\-H\fR
+.IP
+Output an N x 4 matrix, as described above.
+.HP
+\fB\-\-no\-pbs\fR, \fB\-N\fR
+Output a 4 x 4 matrix, as described above.
+With this option,
+a code file is not needed.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Show this help message.
diff --git a/debian/help2man/pbsTrain.1 b/debian/help2man/pbsTrain.1
new file mode 100644
index 0000000..eda9724
--- /dev/null
+++ b/debian/help2man/pbsTrain.1
@@ -0,0 +1,157 @@
+.TH PBSTRAIN "1" "May 2016" "pbsTrain 1.4" "User Commands"
+.SH NAME
+pbsTrain \- Estimate a discrete encoding scheme for probabilistic biological
+.SH DESCRIPTION
+Estimate a discrete encoding scheme for probabilistic biological
+sequences (PBSs) based on training data. Input file should be a
+table of probability vectors, with a row for each distinct vector,
+and a column of counts (positive integers) followed by d columns
+for the elements of the d\-dimensional probability vectors (see
+example below). It may be produced with 'prequel' using the
+\fB\-\-suff\-stats\fR option. Output is a code file that can be used with
+pbsEncode, pbsDecode, etc. By default, a code of size 255 is
+created, so that encoded PBSs can be represented with one byte per
+position (the 256th letter in the code is reserved for gaps). The
+\fB\-\-nbytes\fR option allows larger codes to be created, if desired.
+.PP
+The code is estimated by a two\-part procedure designed to minimize
+the "training error" (defined as the total KL divergence) of the
+encoded training data with respect to the original training data.
+First, a "grid" is defined for the probability simplex,
+partitioning it into regions that intersect "cells" (hypercubes)
+in a matrix in d\-dimensional space. This grid has n "rows" per
+dimension. By default, n is given the largest possible value such
+that the number of simplex regions is no larger than the target
+code size, but smaller values of n can be specified using \fB\-\-nrows\fR.
+Each simplex region is assigned a letter in the code, and the
+representative point for that letter is set equal to the mean
+(weighted by the counts) of all vectors in the training data that
+fall in that region. This can be shown to minimize the training
+error for this initial encoding scheme. (If no vectors fall in a
+region, then the representative point is set equal to the centroid
+of the region, which can be shown to minimize the expected KL
+divergence of points uniformly distributed in the region.)
+.PP
+In the second part of the estimation procedure, the remaining
+letters in the code are defined by a greedy algorithm, which
+attempts to further minimize the training error. Briefly, on
+each step, the simplex region with the largest contribution to the
+total error is identified, and the next letter in the code is
+assigned to that region. In this new encoding, there are multiple
+letters, hence multiple representative points, per region; the
+representative point for a given vector is taken to be the
+closest, in terms of KL divergence, of the representative points
+associated with the simplex region in which that vector falls.
+When a new representative point is added to a region, all
+representative points for that region are reoptimized using a
+k\-means type algorithm. This procedure is repeated, letter by
+letter, until the number of code letters equals the target code
+size.
+.SH EXAMPLE
+.PP
+Generate training data using prequel:
+.IP
+prequel \fB\-\-suff\-stats\fR mammals.fa mytree.mod training
+.TP
+A file called "training.stats" will be generated.
+It will look
+.IP
+something like this:
+.IP
+#count
+.IP
+p(A) p(C) p(G) p(T)
+.IP
+170085
+.IP
+0.043485 0.797886 0.029534 0.129096
+.IP
+158006
+.IP
+0.191119 0.046081 0.695205 0.067595
+.IP
+221937
+.IP
+0.047309 0.122834 0.043852 0.786004
+.IP
+221585
+.IP
+0.781156 0.044520 0.126179 0.048146
+.IP
+159472
+.IP
+0.067254 0.697947 0.045959 0.188840
+.IP
+\&...
+.PP
+Now estimate a code from the training data:
+.IP
+pbsTrain training.stats > mammals.code
+.PP
+The code file contains some metadata followed by a list of code
+indices and representative points, e.g.,
+.IP
+##NROWS = 7
+.IP
+##DIMENSION = 4
+.IP
+##NBYTES = 1
+.IP
+##CODESIZE = 255
+.IP
+# Code generated by pbsTrain, with argument(s) "training.stats"
+.IP
+# acs, Mon Jul 18 23:29:07 2005
+.IP
+# Average training error = 0.001298 bits
+.PP
+Each index of the code is shown below with its representative probability
+vector (p1, p2, ..., pd).
+.IP
+#code_index p1 p2 ...
+0 0.107143 0.107143 0.107143 0.678571
+.IP
+1 0.033226 0.093854 0.031987 0.840933
+.IP
+2 0.000059 0.001645 0.000111 0.998185
+.IP
+3 0.139270 0.021059 0.278993 0.560678
+.IP
+\&...
+.PP
+The reported "average training error" is the training error
+divided by the number of data points (the sum of the counts).
+.SH OPTIONS
+.HP
+\fB\-\-nrows\fR, \fB\-n\fR <n>
+Number of "rows" per dimension in the simplex grid.
+Default
+is maximum possible for code size.
+.HP
+\fB\-\-nbytes\fR, \fB\-b\fR <b>
+.IP
+Number of bytes per encoded probabilistic base (default 1).
+The size of the code will be 256^b \- 1 (one letter in the code
+is reserved for gaps). Values as large as 4 are allowed for
+b, but in the current implementation, performance
+considerations effectively limit it to 2 or 3.
+.HP
+\fB\-\-no\-greedy\fR, \fB\-G\fR
+Skip greedy optimization \fB\-\-\fR just assign a single
+representative point to each region of the probability
+simplex, equal to the (weighted) mean of all vectors from the
+training data that fall in that region.
+.HP
+\fB\-\-no\-train\fR, \fB\-x\fR <dim>
+.IP
+Ignore the data entirely; just use the centroid of each
+simplex partition. The dimension of the simplex must be given
+(<dim>) but no data file is required.
+.HP
+\fB\-\-log\fR, \fB\-l\fR <file>
+.IP
+write log of optimization procedure to specified file.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
diff --git a/debian/help2man/phast.1 b/debian/help2man/phast.1
new file mode 100644
index 0000000..e9567ca
--- /dev/null
+++ b/debian/help2man/phast.1
@@ -0,0 +1,49 @@
+.TH PHAST "1" "May 2016" "phast 1.4" "User Commands"
+.SH NAME
+phast \- phylogenetic analysis with space/time models
+.SH DESCRIPTION
+The PHAST package contains the following programs:
+.TP
+all_dists
+hmm_view phastBias
+.TP
+base_evolve
+indelFit phastCons
+.TP
+chooseLines
+indelHistory phastMotif
+.TP
+clean_genes
+maf_parse phastOdds
+.TP
+consEntropy
+makeHKY phyloBoot
+.TP
+convert_coords
+modFreqs phyloFit
+.TP
+display_rate_matrix
+msa_diff phyloP
+.TP
+dless
+msa_split prequel
+.TP
+dlessP
+msa_view refeature
+.TP
+draw_tree
+pbsDecode stringiphy
+.TP
+eval_predictions
+pbsEncode test
+.TP
+exoniphy
+pbsScoreMatrix tree_doctor
+.TP
+hmm_train
+pbsTrain treeGen
+.TP
+hmm_tweak
+phast
+.IP
+For help, type the program's name followed by \fB\-h\fR in your command line window.
diff --git a/debian/help2man/phastBias.1 b/debian/help2man/phastBias.1
new file mode 100644
index 0000000..9dc96fb
--- /dev/null
+++ b/debian/help2man/phastBias.1
@@ -0,0 +1,172 @@
+.TH PHASTBIAS "1" "May 2016" "phastBias 1.4" "User Commands"
+.SH NAME
+phastBias \- Identify regions of the alignment which are affected by gBGC,
+.SH SYNOPSIS
+The alignment file can be in any of several file formats (see
+\fB\-\-msa\-format\fR). The neutral model must be in the .mod format
+produced by the phyloFit program. The foreground_branch should
+identify a branch of the tree (internal branches can be named
+with tree_doctor \fB\-\-name\-ancestors\fR).
+.SH DESCRIPTION
+Identify regions of the alignment which are affected by gBGC,
+indicated by a cluster of weak\-to\-strong (A/T \-> G/C) substitutions
+amidst a deficit of strong\-to\-weak substitutions on a particular
+branch of the tree. The regions are identified by a phylo\-HMM
+with four states: neutral, conserved, neutral with gBGC, and
+conserved with gBGC.
+.SS OUTPUT:
+phastBias produces a wig file with scores for every position in the
+alignment indicating the probability of being in one of the gBGC
+states. It can also produce gBGC tracts by thresholding this
+probability at 0.5, or a matrix of probabilities for all four states.
+See OUTPUT OPTIONS below.
+.SH OPTIONS
+.SS GENERAL OPTIONS:
+.HP
+\fB\-\-help\fR,\-h
+Print this help message.
+.PP
+TUNING PARAMETER OPTIONS:
+.IP
+gBGC PARAMETERS:
+.HP
+\fB\-\-bgc\fR <B>
+.TP
+The B parameter describes the strength of gBGC.
+It must be > 0.
+.IP
+Too low of a value may yield false positives, as the gBGC model
+becomes indistinguishable from the non\-gBGC model.
+.IP
+Default: 3
+.HP
+\fB\-\-estimate\-bgc\fR <0|1>
+Use "\-\-estimate\-bgc 1" to estimate B by maximum likelihood.
+Default: 0
+.HP
+\fB\-\-bgc\-exp\-length\fR <length>
+.TP
+Set the prior expected length of gBGC tracts.
+This is equivalent to
+.IP
+1/alpha in the parametrization defined by Capra et al, where
+alpha is the rate out of gBGC states.
+.IP
+Default: 1000
+.HP
+\fB\-\-estimate\-bgc\-exp\-length\fR <0|1>
+Use "\-\-estimate\-bgc\-exp\-length 1" to estimate this parameter by an
+.IP
+expectation\-maximization algorithm.
+.IP
+Default: 0
+.HP
+\fB\-\-bgc\-target\-coverage\fR <coverage>
+.IP
+Set the prior for gBGC tract coverage (as a fraction between 0 and 1).
+.IP
+This is represented in the model as beta/(alpha+beta), where beta
+is the rate into the gBGC state, and alpha is the rate out of the
+gBGC state.
+.IP
+Default: 0.01
+.HP
+\fB\-\-estimate\-bgc\-target\-coverage\fR <0|1>
+Use "\-\-estimate\-bgc\-target\-coverage 0" to hold this parameter constant.
+Default: 1 (This is the only parameter estimated by default.)
+.SS CONSERVATION PARAMETERS:
+.PP
+Note: it is not recommended to tune these parameters with phastBias.
+.PP
+Rather, phastCons may be used to determine the best values for rho
+and the transition rates into/out of conserved elements. See
+phastCons \fB\-\-help\fR and the phastCons HOWTO (available online) to learn
+about tuning these parameters.
+.HP
+\fB\-\-rho\fR <rho>
+.TP
+Set the scaling factor for branch lengths in conserved states.
+Rho should
+.IP
+be between 0 and 1.
+.IP
+Default: 0.31
+.HP
+\fB\-\-cons\-exp\-length\fR <length>
+.TP
+Set the prior expected length of conserved elements.
+This parameter is
+.IP
+held constant; if you want to tune it, it is recommended to do this
+with the phastCons program under a non\-gBGC model (see the
+\fB\-\-expected\-length\fR option in phastCons).
+Default: 45
+.HP
+\fB\-\-cons\-target\-coverage\fR <cov>
+.IP
+Set the prior for coverage of conserved elements (as a fraction
+between 0 and 1).
+Like the \fB\-\-cons\-exp\-length\fR above, this parameter
+is also held constant, but can be tuned with phastCons (see
+phastCons \fB\-\-transitions\fR).
+Default: 0.3
+.SS OTHER PARAMETERS:
+.HP
+\fB\-\-scale\fR <scale>
+Set an overall scaling factor for the branch lengths in all states.
+Default: 1
+.HP
+\fB\-\-estimate\-scale\fR <0|1>
+.IP
+Rescale the branches in all states by a scaling factor determined by
+.IP
+maximum likelihood (initialized by \fB\-\-scale\fR above).
+Default: 0
+.HP
+\fB\-\-eqfreqs\-from\-msa\fR <0|1>
+.IP
+Reset equilibrium frequencies of A,C,G,T based on frequencies observed
+in the alignment.
+Otherwise will not be altered from input model.
+Default: 1
+.SS OUTPUT OPTIONS
+.HP
+\fB\-\-output\-tracts\fR <file.gff>
+.IP
+Print a GFF file identifying all regions with posterior probability of
+being in a gBGC state > 0.5.
+.HP
+\fB\-\-posteriors\fR <none|wig|full>
+.IP
+Use this option to control posterior probability output, which is
+written to stdout.
+"none" implies do not output anything; wig outputs
+a standard fixed\-step wiggle file giving the probability that each
+base is assigned to a gBGC state; "full" outputs a table with five
+columns. The first column is the coordinate (1\-based relative to
+the first sequence in the alignment), followed by the probabilities
+of each of the four states: neutral, conserved, gBGC neutral,
+gBGC conserved.
+.IP
+Default: wig
+.HP
+\fB\-\-output\-mods\fR <output_root>
+.IP
+Print out the tree models for all four states to <output_root>.cons.mod,
+<output_root>.neutral.mod, <output_root>.gBGC_cons.mod, and
+<output_root>.gBGC_neutral.mod.
+.HP
+\fB\-\-informative\-fn\fR,\-i <file.gff>
+.IP
+Print a GFF containing regions of the alignment which are informative
+for gBGC. Note: only works properly if foreground branch is a single
+branch (not a group of branches).
+.HP
+\fB\-\-informative\-only\fR,\-o
+.IP
+(To be used with \fB\-\-informative\-fn\fR). Print the informative regions, then
+quit.
+.SH SEE ALSO
+Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A: A Model\-Based Analysis
+of GC\-Biased Gene Conversion in the Human and Chimpanzee Genomes.
+(Manuscript in submission).
diff --git a/debian/help2man/phastCons.1 b/debian/help2man/phastCons.1
new file mode 100644
index 0000000..e3e60f0
--- /dev/null
+++ b/debian/help2man/phastCons.1
@@ -0,0 +1,445 @@
+.TH PHASTCONS "1" "May 2016" "phastCons 1.4" "User Commands"
+.SH NAME
+phastCons \- Identify conserved elements or produce conservation scores, given
+.SH SYNOPSIS
+The alignment file can be in any of several file formats (see
+\fB\-\-msa\-format\fR). The phylogenetic models must be in the .mod format
+produced by the phyloFit program.
+.SH DESCRIPTION
+Identify conserved elements or produce conservation scores, given
+a multiple alignment and a phylo\-HMM. By default, a phylo\-HMM
+consisting of two states is assumed: a "conserved" state and a
+"non\-conserved" state. Separate phylogenetic models can be
+specified for these two states, e.g.,
+.IP
+phastCons myfile.ss cons.mod,noncons.mod > scores.wig
+.PP
+or a single model can be given for the non\-conserved state, e.g.,
+.IP
+phastCons myfile.ss \fB\-\-rho\fR 0.5 noncons.mod > scores.wig
+.PP
+in which case the model for the conserved state will be obtained
+by multiplying all branch lengths by the scaling parameter rho (0
+< rho < 1). If the \fB\-\-rho\fR option is not used, rho will be set to
+its default value of 0.3.
+.PP
+By default, the phylogenetic models will be left unaltered, but if
+the \fB\-\-estimate\-trees\fR option is used, e.g.,
+.IP
+phastCons myfile.ss init.mod \fB\-\-estimate\-trees\fR newtree > scores.wig
+.PP
+then the phylogenetic models for the two states will be estimated
+from the data, and the given tree model (there must be only one in
+this case) will be used for initialization only. It is also
+possible to estimate only the scale factor \fB\-\-rho\fR, using the
+\fB\-\-estimate\-rho\fR option.
+The transition probabilities for the HMM can either be specified
+at the command line or estimated from the data using an EM
+algorithm. To specify them at the command line, use either the
+\fB\-\-transitions\fR option or the \fB\-\-target\-coverage\fR and
+\fB\-\-expected\-length\fR options. The recommended method is to use
+\fB\-\-target\-coverage\fR and \fB\-\-expected\-length\fR, e.g.,
+.IP
+phastCons \fB\-\-target\-coverage\fR 0.25 \fB\-\-expected\-length\fR 12
+myfile.ss cons.mod,noncons.mod > scores.wig
+.SS The program produces two main types of output.
+The primary
+output, sent to stdout in fixed\-step WIG format
+(http://genome.ucsc.edu/goldenPath/help/wiggle.html), is a set of
+base\-by\-base conservation scores. The score at each base is equal
+to the posterior probability that that base was "generated" by the
+conserved state of the phylo\-HMM. The scores are reported in the
+coordinate frame of a designated reference sequence (see
+\fB\-\-refidx\fR), which is by default the first sequence in the
+alignment. They can be suppressed with the \fB\-\-no\-post\-probs\fR
+option. The secondary type of output, activated with the
+\fB\-\-most\-conserved\fR (aka \fB\-\-viterbi\fR) option, is a set of discrete
+conserved elements. These elements are output in either BED or GFF
+format, also in the coordinate system of the reference sequence
+(see \fB\-\-most\-conserved\fR). They can be assigned log\-odds scores
+using the \fB\-\-score\fR option.
+.PP
+Other uses are also supported, but will not be described in detail
+here. For example, it is possible to produce conservation scores
+and conserved elements using a k\-state phylo\-HMM of the kind
+described by Felsenstein and Churchill (1996) (see \fB\-\-FC\fR), and it
+is possible to produce a "coding potential" score instead of a
+conservation score (see \fB\-\-coding\-potential\fR). It is also possible
+to give the program a custom HMM and to specify any subset of its
+states to use for prediction (see \fB\-\-hmm\fR and \fB\-\-states\fR).
+.PP
+See the phastCons HOWTO for additional details.
+.SH EXAMPLE
+.PP
+1. Given phylogenetic models for conserved and nonconserved regions
+and HMM transition parameters, compute a set of conservation scores.
+.IP
+phastCons \fB\-\-transitions\fR 0.01,0.01 mydata.ss cons.mod,noncons.mod
+\f(CW> scores.wig\fR
+.PP
+2. Similar to (1), but define the conserved model as a scaled
+version of the nonconserved model, with rho=0.4 as the scaling
+parameter. Also predict conserved elements as well as
+conservation scores, and assign log\-odds scores to predictions.
+.IP
+phastCons \fB\-\-transitions\fR 0.01,0.01 \fB\-\-most\-conserved\fR mostcons.bed
+\fB\-\-score\fR \fB\-\-rho\fR 0.4 mydata.ss noncons.mod > scores.wig
+.PP
+(if output file were "mostcons.gff," then output would be in
+GFF instead of BED format)
+.PP
+3. This time, estimate the parameter rho from the data.
+Suppress both the scores and the conserved elements.
+Specify the
+transition probabilities using \fB\-\-target\-coverage\fR and
+\fB\-\-expected\-length\fR instead of \fB\-\-transitions\fR.
+.IP
+phastCons \fB\-\-target\-coverage\fR 0.25 \fB\-\-expected\-length\fR 12
+\fB\-\-estimate\-rho\fR newtree \fB\-\-no\-post\-probs\fR mydata.ss noncons.mod
+.PP
+4. This time estimate all free parameters of the tree models.
+.IP
+phastCons \fB\-\-target\-coverage\fR 0.25 \fB\-\-expected\-length\fR 12
+\fB\-\-estimate\-trees\fR newtree \fB\-\-no\-post\-probs\fR mydata.ss noncons.mod
+.PP
+5. Estimate the state\-transition parameters but not the tree models.
+Output the conservation scores but not the conserved
+elements.
+.IP
+phastCons mydata.ss cons.mod,noncons.mod > scores.wig
+.PP
+6. Estimate just the expected\-length parameter and also estimate rho.
+.IP
+phastCons \fB\-\-target\-coverage\fR 0.25 \fB\-\-estimate\-rho\fR newtree
+mydata.ss noncons.mod > scores.wig
+.SH OPTIONS
+.SS Tree models
+.HP
+\fB\-\-rho\fR, \fB\-R\fR <rho>
+.IP
+Set the *scale* (overall evolutionary rate) of the model for
+the conserved state to be <rho> times that of the model for
+the non\-conserved state (0 < <rho> < 1; default 0.3). If used
+with \fB\-\-estimate\-trees\fR or \fB\-\-estimate\-rho\fR, the specified value
+will be used for initialization only (rho will be
+estimated). This option is ignored if two tree models are
+given.
+.HP
+\fB\-\-estimate\-trees\fR, \fB\-T\fR <fname_root>
+Estimate free parameters of tree models and write new models
+to <fname_root>.cons.mod and <fname_root>.noncons.mod.
+.HP
+\fB\-\-estimate\-rho\fR, \fB\-O\fR <fname_root>
+.IP
+Like \fB\-\-estimate\-trees\fR, but estimate only the parameter rho.
+.HP
+\fB\-\-gc\fR, \fB\-G\fR <val>
+(Optionally use with \fB\-\-estimate\-trees\fR or \fB\-\-estimate\-rho\fR)
+Assume a background nucleotide distribution consistent with
+the given average G+C content (0 < <val> < 1) when estimating
+tree models. (The frequencies of G and C will be set to
+<val>/2 and the frequencies of A and T will be set to
+(1\-<val>)/2.) This option overrides the default behavior of
+estimating the background distribution from the data (if
+\fB\-\-estimate\-trees\fR) or obtaining them from the input model (if
+\fB\-\-estimate\-rho\fR).
+.HP
+\fB\-\-nrates\fR, \fB\-k\fR <nrates> | <nrates_conserved,nrates_nonconserved>
+(Optionally use with a discrete\-gamma model and \fB\-\-estimate\-trees\fR)
+Assume the specified number of rate categories, instead of the
+number given in the *.mod file. The shape parameter 'alpha' will
+be as given in the *.mod file. In the case of the default
+two\-state HMM, two values can be specified, for the numbers of
+rates for the conserved and the nonconserved states, resp.
+.SS State\-transition parameters
+.HP
+\fB\-\-transitions\fR, \fB\-t\fR [~]<mu>,<nu>
+.IP
+Fix the transition probabilities of the two\-state HMM as
+specified, rather than estimating them by maximum likelihood.
+Alternatively, if first character of argument is '~', estimate
+parameters, but initialize to specified values. The argument
+<mu> is the probability of transitioning from the conserved to
+the non\-conserved state, and <nu> is the probability of the
+reverse transition. The probabilities of self transitions are
+thus 1\-<mu> and 1\-<nu> and the expected lengths of conserved
+and nonconserved elements are 1/<mu> and 1/<nu>, respectively.
+.HP
+\fB\-\-target\-coverage\fR, \fB\-C\fR <gamma>
+.IP
+(Alternative to \fB\-\-transitions\fR) Constrain transition parameters
+such that the expected fraction of sites in conserved elements
+is <gamma> (0 < <gamma> < 1). This is a *prior* rather than
+*posterior* expectation and assumes stationarity of the
+state\-transition process. Adding this constraint causes the
+ratio mu/nu to be fixed at (1\-<gamma>)/<gamma>. If used with
+\fB\-\-expected\-length\fR, the transition probabilities will be
+completely fixed; otherwise the expected\-length parameter
+<omega> will be estimated by maximum likelihood.
+\fB\-\-expected\-length\fR, \fB\-E\fR [~]<omega>
+{\-\-expected\-lengths also allowed,
+for backward compatibility}
+.IP
+(For use with \fB\-\-target\-coverage\fR, alternative to \fB\-\-transitions\fR)
+Set transition probabilities such that the expected length of
+a conserved element is <omega>. Specifically, the parameter
+mu is set to 1/<omega>. If preceded by '~', <omega> will be
+estimated, but will be initialized to the specified value.
+.SS Input/output
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR PHYLIP|FASTA|MPM|SS|MAF
+.TP
+Alignment file format.
+Default is to guess format based on
+.TP
+file contents.
+Note that the msa_view program can be used to
+.IP
+convert between formats.
+.HP
+\fB\-\-viterbi\fR [alternatively \fB\-\-most\-conserved]\fR, \fB\-V\fR <fname>
+Predict discrete elements using the Viterbi algorithm and
+write to specified file. Output is in BED format, unless
+<fname> has suffix ".gff", in which case output is in GFF.
+.HP
+\fB\-\-score\fR, \fB\-s\fR
+(Optionally use with \fB\-\-viterbi\fR) Assign a log\-odds score to
+each prediction.
+.HP
+\fB\-\-lnl\fR, \fB\-L\fR <fname>
+.IP
+Compute total log likelihood using the forward algorithm and
+write to specified file.
+.HP
+\fB\-\-no\-post\-probs\fR, \fB\-n\fR
+Suppress output of posterior probabilities.
+Useful if only discrete elements or likelihood is of interest.
+.HP
+\fB\-\-log\fR, \fB\-g\fR <log_fname>
+.IP
+(Optionally use when estimating free parameters) Write log of
+optimization procedure to specified file.
+.HP
+\fB\-\-refidx\fR, \fB\-r\fR <refseq_idx>
+Use coordinate frame of specified sequence in output.
+Default
+.IP
+value is 1, first sequence in alignment; 0 indicates
+coordinate frame of entire multiple alignment.
+.HP
+\fB\-\-seqname\fR, \fB\-N\fR <name>
+(Optionally use with \fB\-\-viterbi\fR) Use specified string
+for 'seqname' (GFF) or 'chrom' field in output file. Default
+is obtained from input file name (double filename root, e.g.,
+"chr22" if input file is "chr22.35.ss").
+.HP
+\fB\-\-idpref\fR, \fB\-P\fR <name>
+.IP
+(Optionally use with \fB\-\-viterbi\fR) Use specified string as
+prefix of generated ids in output file. Can be used to ensure
+ids are unique. Default is obtained from input file name
+(single filename root, e.g., "chr22.35" if input file is
+"chr22.35.ss").
+.HP
+\fB\-\-quiet\fR, \fB\-q\fR
+Proceed quietly (without updates to stderr).
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
+(Indels) [experimental]
+.HP
+\fB\-\-indels\fR, \fB\-I\fR
+.IP
+Expand HMM state space to model indels as described in Siepel
+& Haussler (2004).
+.HP
+\fB\-\-max\-micro\-indel\fR, \fB\-Y\fR <length>
+(Optionally use with \fB\-\-indels\fR) Maximum length of an alignment
+gap to be considered a "micro\-indel" and therefore
+addressed by the indel model. Gaps longer than this threshold
+will be treated as missing data. Default value is 20.
+.HP
+\fB\-\-indel\-params\fR, \fB\-D\fR [~]<alpha_0,beta_0,tau_0,alpha_1,beta_1,tau_1>
+.IP
+(Optionally use with \fB\-\-indels\fR and default two\-state HMM) Fix
+the indel parameters at (alpha_0, beta_0, tau_0) for the
+conserved state and at (alpha_1, beta_1, tau_1) for the
+non\-conserved state, rather than estimating them by maximum
+likelihood. Alternatively, if first character of argument is
+\&'~', estimate parameters, but initialize with specified
+values. Alpha_j is the rate of insertion events per
+substitution per site in state j (typically ~0.05), beta_j is
+the rate of deletion events per substitution per site in state
+j (typically ~0.05), and tau_j is approximately the inverse
+of the expected indel length in state j (typically 0.2\-0.5).
+.HP
+\fB\-\-indels\-only\fR, \fB\-J\fR
+Like \fB\-\-indels\fR but force the use of a single\-state HMM.
+This
+option allows the effect of the indel model in isolation to be
+observed. Implies \fB\-\-no\-post\-probs\fR. Use with \fB\-\-lnl\fR.
+(Felsenstein/Churchill model) [rarely used]
+.HP
+\fB\-\-FC\fR, \fB\-X\fR
+.IP
+(Alternative to \fB\-\-hmm\fR; specify only one *.mod file with this
+option) Use an HMM with a state for every rate
+category in the given phylogenetic model, and transition
+probabilities defined by an autocorrelation parameter lambda
+(as described by Felsenstein and Churchill, 1996). A rate
+constant for each state (rate category) will be multiplied by
+the branch lengths of the phylogenetic model, to create a
+"scaled" version of the model for that state. If the
+phylogenetic model was estimated using Yang's discrete gamma
+method (\fB\-k\fR option to phyloFit), then the rate constants will
+be defined according to the estimated shape parameter 'alpha',
+as described by Yang (1994). Otherwise, a nonparameteric
+model of rate variation must have been used (\fB\-K\fR option to
+phyloFit), and the rate constants will be as defined
+(explicitly) in the *.mod file. By default, the parameter
+lambda will be estimated by maximum likelihood (see \fB\-\-lambda\fR).
+.HP
+\fB\-\-lambda\fR, \fB\-l\fR [~]<lambda>
+.IP
+(Optionally use with \fB\-\-FC\fR) Fix lambda at the
+specified value rather than estimating it by maximum
+likelihood. Alternatively, if first character is '~',
+estimate but initialize at specified value. Allowable range
+is 0\-1. With k rate categories, the transition probability
+between state i and state j will be lambda * I(i == j) +
+(1\-lambda)/k, where I is the indicator function. Thus, lambda
+= 0 implies no autocorrelation and lambda = 1 implies perfect
+autocorrelation.
+(Coding potential) [experimental]
+.HP
+\fB\-\-coding\-potential\fR, \fB\-p\fR
+.IP
+Use parameter settings that cause output to be interpretable
+as a coding potential score. By default, a simplified version
+of exoniphy's phylo\-HMM is used, with a noncoding (background)
+state, a conserved non\-coding (CNS) state, and states for the
+three codon positions. This option implies \fB\-\-catmap\fR "NCATS=4;
+CNS 1; CDS 2\-4" \fB\-\-hmm\fR <default\-HMM\-file> \fB\-\-states\fR CDS
+\fB\-\-reflect\-strand\fR background,CNS and a set of default *.mod
+files (all of which can be overridden). This option can be
+used with or without \fB\-\-indels\fR.
+.HP
+\fB\-\-extrapolate\fR, \fB\-e\fR <phylog.nh> | default
+.IP
+Extrapolate to a larger set of species based on the given
+phylogeny (Newick\-format). The trees in the given tree models
+(*.mod files) must be subtrees of the larger phylogeny. For
+each tree model M, a copy will be created of the larger
+phylogeny, then scaled such that the total branch length of
+the subtree corresponding to M's tree equals the total branch
+length of M's tree; this new version will then be used in
+place of M's tree. (Any species name present in this tree but
+not in the data will be ignored.) If the string "default"
+is given instead of a filename, then a phylogeny for 25
+vertebrate species, estimated from sequence data for Target 1
+(CFTR) of the NISC Comparative Sequencing Program (Thomas et
+al., 2003), will be assumed.
+.HP
+\fB\-\-alias\fR, \fB\-A\fR <alias_def>
+.IP
+Alias names in input alignment according to given definition,
+e.g., "hg17=human; mm5=mouse; rn3=rat". Useful with default
+*.mod files, e.g., with \fB\-\-coding\-potential\fR. (Default models
+use generic common names such as "human", "mouse", and
+"rat". This option allows a mapping to be established
+between the leaves of trees in these files and the sequences
+of an alignment that uses an alternative naming convention.)
+.SS Custom HMMs [rarely used]
+.HP
+\fB\-\-hmm\fR, \fB\-H\fR <hmm_fname>
+.IP
+Name of HMM file explicitly defining the probabilities of all
+state transitions. States in the file must correspond in
+number and order to phylogenetic models in <mod_fname_list>.
+Expected file format is as produced by 'hmm_train.'
+.HP
+\fB\-\-catmap\fR, \fB\-c\fR <fname>|<string>
+(Optionally use with \fB\-\-hmm\fR)
+Mapping of feature types to category
+numbers.
+Can give either a filename or an "inline" description
+of a simple category map, e.g., \fB\-\-catmap\fR "NCATS = 3 ; CDS 1\-3".
+.HP
+\fB\-\-states\fR, \fB\-S\fR <state_list>
+.IP
+States of interest in the phylo\-HMM, specified by number
+(indexing starts with 0), or if \fB\-\-catmap\fR, by category name.
+Default value is 1. Choosing \fB\-\-states\fR "0,1,2" will cause
+output of the sum of the posterior probabilities for states 0,
+1, and 2, and/or of regions in which the Viterbi path
+coincides with (any of) states 0, 1, or 2 (see \fB\-\-viterbi\fR).
+.HP
+\fB\-\-reflect\-strand\fR, \fB\-U\fR <pivot_states>
+.IP
+(Optionally use with \fB\-\-hmm\fR) Given an HMM describing the
+forward strand, create a larger HMM that allows for features
+on both strands by "reflecting" the original HMM about the
+specified "pivot" states. The new HMM will be used for
+prediction on both strands. States can be specified by number
+(indexing starts with 0), or if \fB\-\-catmap\fR, by category name.
+.SS Missing data [rarely used]
+.HP
+\fB\-\-require\-informative\fR, \fB\-M\fR <states>
+Require "informative" columns (i.e., columns with more than
+two non\-missing\-data characters, excluding sequences specified
+by \fB\-\-not\-informative\fR) in specified HMM states, to help
+eliminate false positive predictions. States can be specified
+by number (indexing starts with 0) or, if \fB\-\-catmap\fR is used, by
+category name. Non\-informative columns will be given emission
+probabilities of zero. By default, this option is active,
+with <states> equal to the set of states of interest for
+prediction (as specified by \fB\-\-states\fR). Use "none" to disable
+completely.
+.HP
+\fB\-\-not\-informative\fR, \fB\-F\fR <list>
+.IP
+Do not consider the specified sequences (listed by name) when
+deciding whether a column is informative. This option may be
+useful when sequences are present that are very close to the
+reference sequence and thus do not contribute much in the way
+of phylogenetic information. E.g., one might use
+"\-\-not\-informative chimp" with a human\-referenced multiple
+alignment including chimp sequence, to avoid false\-positive
+predictions based only on human/chimp alignments (can be a
+problem, e.g., with \fB\-\-coding\-potential\fR).
+.HP
+\fB\-\-ignore\-missing\fR, \fB\-z\fR
+.IP
+(For use when estimating transition probabilities) Ignore
+regions of missing data in all sequences but the reference
+sequence (excluding sequences specified by \fB\-\-not\-informative\fR)
+when estimating transition probabilities. Can help avoid
+too\-low estimates of <mu> and <nu> or too\-high estimates of
+<lambda>. Warning: this option should not be used with
+\fB\-\-viterbi\fR because coordinates in output will be
+unrecognizable.
+.SH SEE ALSO
+J. Felsenstein and G. Churchill.
+1996. A hidden Markov model
+approach to variation among sites in rate of evolution.
+Mol. Biol. Evol., 13:93\-104.
+A. Siepel, G. Bejerano, J. S. Pedersen, et al.
+2005.
+.PP
+Evolutionarily conserved elements in vertebrate, insect, worm,
+and yeast genomes. Genome Res. (in press)
+A. Siepel and D. Haussler.
+2004. Computational identification of
+evolutionarily conserved exons.
+Proc. 8th Annual Int'l Conf.
+on Research in Computational Biology (RECOMB '04), pp. 177\-186.
+.PP
+J. Thomas et al.
+2003. Comparative analyses of multi\-species
+sequences from targeted genomic regions.
+Nature 424:788\-793.
+.PP
+Z. Yang. 1994. Maximum likelihood phylogenetic estimation from
+DNA sequences with variable rates over sites: approximate
+methods. J. Mol. Evol., 39:306\-314.
diff --git a/debian/help2man/phastMotif.1 b/debian/help2man/phastMotif.1
new file mode 100644
index 0000000..73dd74c
--- /dev/null
+++ b/debian/help2man/phastMotif.1
@@ -0,0 +1,112 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH PHASTMOTIF "1" "May 2016" "phastMotif 1.4" "User Commands"
+.SH NAME
+phastMotif \- Predicts motifs from a set of multiple alignments. Uses
+.SH DESCRIPTION
+Predicts motifs from a set of multiple alignments. Uses
+an EM algorithm similar to that of MEME, but a motif is
+defined by phylogenetic models rather than multinomial
+distributions. The specified multiple alignments may
+actually be single sequences (see \fB\-m\fR). Various parameters
+control the strategy for initialization (see below).
+Currently, the F81 substitution model is assumed.
+.SH USAGE
+phastMotif [\-t <treefile>] [OPTIONS] <msa_list>
+.SH OPTIONS
+.HP
+\fB\-t\fR <file> (Required unless \fB\-m\fR or \fB\-p\fR) Use specified tree topology for
+all phylogenetic models (Newick format).
+.TP
+\fB\-i\fR <fmt>
+Input format for alignment. May be FASTA, PHYLIP, MPM, SS,
+or MAF (default FASTA).
+.HP
+\fB\-b\fR <file> Read background model from specified file (.mod format).
+.IP
+By default, the background model is estimated
+in a preprocessing step, by pooling all data.
+.TP
+\fB\-s\fR
+Estimate a separate background model for each multiple alignment.
+(Not yet implemented.)
+.HP
+\fB\-k\fR <size> Learn motifs of the specified size (default is 10).
+.TP
+\fB\-B\fR <n>
+Report best <n> motifs (default 3).
+.TP
+\fB\-m\fR
+MEME mode. Use multinomial rather than phylogenetic
+models. Causes multiple alignments to be ignored \fB\-\-\fR any
+gaps are discarded and all sequences are assumed
+independent.
+.HP
+\fB\-d\fR <+lst> Use the discriminative training method of Segal et
+al. (RECOMB'02), rather than EM.
+The specified list
+.IP
+should contain the filenames from msa_list that are to
+be considered *positive* examples (containing the
+desired motif); all others will be considered negative
+examples. Can be used with or without \fB\-m\fR.
+\fB\-p\fR
+Use "profile" models rather than phylogenetic models
+(characters in each alignment column assumed
+independent). The resulting model is a hybrid of the
+full model and MEME's model. Essentially, it uses the
+multiple alignments but not the phylogeny. NOT YET IMPLEMENTED.
+\fB\-n\fR <n>
+Perform <n> random restarts and report the motif with highest
+likelihood. Default number is 10. Ignored with \fB\-I\fR, \fB\-P\fR, and
+\fB\-R\fR unless \fB\-S\fR is specified (see below).
+.HP
+\fB\-I\fR <mlst> Run the algorithm after a "soft" initialization with
+.IP
+each of the consensus sequences in the specified list.
+At each position, <pc> pseudocounts (see \fB\-c\fR) are given
+to the consensus base and 1 pseudocount to all other
+bases. Each string must have length at most equal to
+the size of the motif. If shorter, it is used as a
+"seed" for a motif, with flanking positions treated as
+wildcards.
+\fB\-P\fR <x,y>
+Initialize with the x most prevalent y\-tuples. A soft
+initialization is performed, as above. If y is less
+than the motif size, y\-tuples are used as a "seed" for
+a motif, as above.
+\fB\-R\fR <x,y>
+Initialize with a random sample of x y\-tuples. A soft
+initialization is performed, as above. If y is less
+than the motif size, y\-tuples are used as a "seed" for
+a motif, as above.
+\fB\-w\fR <n>
+(for use with \fB\-I\fR, \fB\-P\fR, \fB\-R\fR) Winnow initialization sequences
+to the top <n> based on the unmaximized likelihood.
+.TP
+\fB\-c\fR <pc>
+(for use with \fB\-I\fR, \fB\-P\fR, \fB\-R\fR) Number of pseudocounts for
+consensus bases (default 5).
+\fB\-S\fR
+(for use with \fB\-I\fR, \fB\-P\fR, \fB\-R\fR) Instead of doing a deterministic
+initialization based on a consensus sequence, sample
+parameters from a Dirichlet distribution defined by the
+pseudocounts (see \fB\-c\fR). In this case, random restarts
+are performed, as specified by \fB\-n\fR.
+.HP
+\fB\-o\fR <pref> Use the specified prefix for all output files (dflt. "phastm").
+\fB\-H\fR
+Produce HTML formatted output, in addition to ordinary output.
+One file is produced per predicted motif, as well as a
+single HTML\-formatted summary file.
+.TP
+\fB\-D\fR
+Produce a BED file with predicted motifs, for use in the
+UCSC browser. Currently, sequence names must be
+formatted such as "chr10:102553847\-102554897+", with
+the final '+' or '\-' indicating strand.
+.TP
+\fB\-x\fR
+(For use with \fB\-H\fR or \fB\-D\fR) Suppress ordinary output to stdout.
+.TP
+\fB\-h\fR
+Print this help message.
diff --git a/debian/help2man/phastOdds.1 b/debian/help2man/phastOdds.1
new file mode 100644
index 0000000..3795b7a
--- /dev/null
+++ b/debian/help2man/phastOdds.1
@@ -0,0 +1,140 @@
+.TH PHASTODDS "1" "May 2016" "phastOdds 1.4" "User Commands"
+.SH NAME
+phastOdds \- Compute log-odds scores based on two phylogenetic models or phylo-HMMs,
+.SH DESCRIPTION
+Compute log\-odds scores based on two phylogenetic models or phylo\-HMMs,
+one for features of interest (e.g., coding exons, conserved regions)
+and one for background. Will either (1) compute a score for each
+feature in an input set, and output the same set of features with
+scores; or (2) output a separate score for each position in fixed\-step
+WIG format (http://genome.ucsc.edu/goldenPath/help/wiggle.html); or (3)
+compute scores in a sliding window of designated size, and output a
+three\-column file, with the index of the center of each window followed
+by the score for that window on the positive strand, then the score for
+that window on the negative strand. The default is to assume a
+reference sequence alignment, with the reference sequence appearing
+first; feature coordinates are assumed to be defined with respect to
+the reference sequence (see \fB\-\-refidx\fR).
+.SH SYNOPSIS
+.B phastOdds
+[OPTIONS]
+\fB\-\-background\-mods\fR <bmods> [\-\-background\-hmm <bhmm>]
+\fB\-\-feature\-mods\fR <fmods> [\-\-feature\-hmm <fhmm>]
+( \fB\-\-features\fR <feats> | \fB\-\-window\fR <size> )
+<alignment>
+.PP
+Arguments <bmods> and <fmods> should be comma\-delimited lists of
+phylogenetic models in .mod format (as produced by phyloFit), <feats>
+may be in GFF, BED, or genepred format, and <alignment> may be in FASTA
+format or an alternative format specified by \fB\-\-msa\-format\fR. HMM files
+should be in the format used by exoniphy.
+.SH EXAMPLE
+(See below for more details on options)
+.PP
+1. Compute conservation scores for features in a GFF file, based on a
+
+model for conserved sites (conserved.mod) vs. a model of neutral
+evolution (neutral.mod). (These models may be estimated with
+phyloFit or phastCons.)
+.IP
+phastOdds \fB\-\-background\-mods\fR neutral.mod \fB\-\-feature\-mods\fR conserved.mod
+\fB\-\-features\fR features.gff alignment.fa > scores.gff
+.PP
+Features could alternatively be specified in BED or genepred format
+(format will be auto\-recognized). The program can be made to
+produce BED\-formatted output with \fB\-\-output\-bed\fR.
+.PP
+2. Compute conservation scores in a sliding window of size 100.
+.IP
+phastOdds \fB\-\-background\-mods\fR neutral.mod \fB\-\-feature\-mods\fR conserved.mod
+\fB\-\-window\fR 100 alignment.fa > scores.dat
+.PP
+(Window is advanced one site at a time.
+Window boundaries are
+defined in the coordinate frame of the multiple alignment, but
+center coordinates are converted to the frame of the reference
+sequence as they are output.)
+.PP
+3. Compute a "coding potential" score for features in a BED file, based
+on a phylo\-HMM for coding regions versus a phylo\-HMM for noncoding
+DNA, with states for conserved and nonconserved sequences.
+.IP
+phastOdds \fB\-\-background\-mods\fR codon1.mod,codon2.mod,codon3.mod
+\fB\-\-background\-hmm\fR coding.hmm
+\fB\-\-feature\-mods\fR neutral.mod,conserved\-noncoding.mod
+\fB\-\-feature\-hmm\fR noncoding.hmm
+\fB\-\-features\fR features.bed \fB\-\-output\-bed\fR alignment.fa > scores.bed
+.SH OPTIONS
+.HP
+\fB\-\-background\-mods\fR, \fB\-b\fR <backgd_mods>
+.IP
+(Required) Comma\-delimited list of tree model (*.mod) files for
+background. If used with \fB\-\-background\-hmm\fR, order of models must
+correspond to order of states in HMM.
+.HP
+\fB\-\-background\-hmm\fR, \fB\-B\fR <backgd.hmm>
+.TP
+HMM for background.
+If there is only one backgound tree
+.IP
+model, a trivial (single\-state) HMM will be assumed.
+.HP
+\fB\-\-feature\-mods\fR, \fB\-f\fR <feat_mods>
+(Required) Comma\-delimited list of tree model (*.mod) files for
+features. If used with \fB\-\-feature\-hmm\fR, order of models must
+correspond to order of states in HMM.
+.HP
+\fB\-\-feature\-hmm\fR, \fB\-F\fR <feat.hmm>
+HMM for features.
+If there is only one tree model for
+features, a trivial (single\-state) HMM will be assumed.
+.HP
+\fB\-\-features\fR, \fB\-g\fR <feats.gff>
+.IP
+(Required unless \fB\-w\fR or \fB\-y\fR) File defining features to be scored
+(GFF, BED, or genepred).
+.HP
+\fB\-\-window\fR, \fB\-w\fR <size>
+(Can be used instead of \fB\-g\fR or \fB\-y\fR) Compute scores in a sliding
+window of the specified size.
+.HP
+\fB\-\-base\-by\-base\fR, \fB\-y\fR
+.IP
+(Can be used instead of \fB\-g\fR or \fB\-y\fR) Output base\-by\-base scores, in
+the coordinate frame of the reference sequence (or of the sequence
+specified by \fB\-\-refidx\fR). Output is in fixed\-step WIG format
+(http://genome.ucsc.edu/goldenPath/help/wiggle.html). This option
+can only be used with individual phylogenetic models, not with sets
+of models and a (nontrivial) HMM.
+.HP
+\fB\-\-window\-wig\fR, \fB\-W\fR <size>
+.IP
+(Can be used instead of \fB\-g\fR or \fB\-y\fR) Like \fB\-\-window\fR but outputs scores
+in fixed\-step WIG format, as with \fB\-\-base\-by\-base\fR. Scores for the
+positive strand only are output.
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR <type>
+.TP
+Input format for alignment.
+May be FASTA, PHYLIP, MPM, SS, or
+.IP
+MAF (default is to guess format from file contents).
+.HP
+\fB\-\-refidx\fR, \fB\-r\fR <ref_seq>
+Index of reference sequence for coordinates.
+Use 0 to
+indicate the coordinate system of the alignment as a whole.
+Default is 1, for first sequence.
+.HP
+\fB\-\-output\-bed\fR, \fB\-d\fR
+.IP
+(For use with \fB\-g\fR) Generate output in bed format rather than GFF.
+.HP
+\fB\-\-verbose\fR, \fB\-v\fR
+Verbose mode.
+Print messages to stderr describing what the
+program is doing.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
diff --git a/debian/help2man/phyloBoot.1 b/debian/help2man/phyloBoot.1
new file mode 100644
index 0000000..a569a2b
--- /dev/null
+++ b/debian/help2man/phyloBoot.1
@@ -0,0 +1,172 @@
+.TH PHYLOBOOT "1" "May 2016" "phyloBoot 1.4" "User Commands"
+.SH NAME
+phyloBoot \- Generate simulated alignment data by parametric or nonparametric
+.SH DESCRIPTION
+Generate simulated alignment data by parametric or nonparametric
+bootstrapping, and/or estimate errors in phylogenetic model parameters.
+When estimating errors in parameters, the tree topology is not inferred
+\fB\-\-\fR estimated errors are conditional on the given topology.
+.PP
+If a model is given in the form of a .mod file (<model_fname>), then
+parametric bootstrapping is performed \fB\-\-\fR i.e., synthetic data sets are
+drawn from the distribution defined by the model. Otherwise, the input
+file is assumed to be a multiple alignment, and non\-parametric
+bootstrapping is performed \fB\-\-\fR i.e., sites are drawn (with replacement)
+from the empirical distribution defined by the given alignment.
+.PP
+The default behavior is to produce simulated alignments, estimate model
+parameters for each one, and then write a table to stdout with a row
+for each parameter and columns for the mean, standard deviation
+(approximate standard error), median, minimum, and maximum of estimated
+values, plus the boundaries of 95%% and 90%% confidence intervals.
+.PP
+The \fB\-\-alignments\-only\fR option, however, allows the parameter estimation
+step to be bypassed entirely, and the program to be used simply to
+generate simulated data sets.
+See usage for phyloFit for additional details on tree\-building
+options.
+.SH EXAMPLE
+.PP
+(See below for more details on options)
+.PP
+1. Estimation of parameter errors by parametric bootstrapping.
+.IP
+phyloBoot \fB\-\-nreps\fR 500 \fB\-\-nsites\fR 10000 mymodel.mod > par_errors
+.PP
+2. Estimation of parameter errors by nonparametric bootstrapping.
+.IP
+phyloBoot \fB\-\-nreps\fR 500 \fB\-\-nsites\fR 10000
+\fB\-\-tree\fR "((human,chimp),(mouse,rat))" myalignment.fa >
+nonpar_errors
+.PP
+3. Parametric generation of simulated data.
+.IP
+phyloBoot mymodel.mod \fB\-\-alignments\-only\fR pardata
+\fB\-\-nreps\fR 500 \fB\-\-nsites\fR 10000
+.PP
+4. Nonparametric generation of simulated data.
+.IP
+phyloBoot myalignment.fa \fB\-\-alignments\-only\fR nonpardata
+\fB\-\-nreps\fR 500 \fB\-\-nsites\fR 10000
+.SH OPTIONS
+.SS bootstrapping options
+.HP
+\fB\-\-nsites\fR, \fB\-L\fR <number>
+Number of sites in sampled alignments.
+If an alignment is
+.IP
+given (non\-parametric case), default is number of sites in
+alignment, otherwise default is 1000.
+.HP
+\fB\-\-nreps\fR, \fB\-n\fR <number>
+Number of replicates.
+Default is 100.
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
+.TP
+(non\-parametric case only)
+Alignment format. Default is to guess
+format from file contents.
+.HP
+\fB\-\-alignments\-only\fR, \fB\-a\fR <fname_root>
+Generate alignments and write them to files with given filename
+root, but do not estimate parameters.
+.HP
+\fB\-\-dump\-mods\fR, \fB\-d\fR <fname_root>
+.IP
+Dump .mod files for individual estimated models (one for each
+replicate).
+.HP
+\fB\-\-dump\-samples\fR, \fB\-m\fR <fname_root>
+.IP
+Dump simulated alignments to files with given filename root.
+Similar to \fB\-\-alignments\-only\fR but does not disable parameter
+estimation.
+.HP
+\fB\-\-dump\-format\fR, \fB\-o\fR FASTA|PHYLIP|MPM|SS.
+.IP
+(For use with \fB\-\-alignments\-only\fR or \fB\-\-dump\-samples\fR) File format to
+use when dumping raw alignments. Default FASTA.
+.HP
+\fB\-\-read\-mods\fR, \fB\-R\fR <fname_list>
+Read estimated models from list of filenames instead of generating
+alignments and estimating parameters. fname_list can be commadelimited list of files, or, if preceded by a '*', the name of a
+file containing the file names (one per line). Can be used to compute
+statistics for replicates that have been processed separately (see
+\fB\-\-alignments\-only\fR). When this option is used, the primary argument
+to the program (<model_fname>|<msa_fname>) will be ignored.
+.HP
+\fB\-\-output\-average\fR, \fB\-A\fR <fname>
+Output a tree model representing the average of all input
+models to the specified file.
+.HP
+\fB\-\-quiet\fR, \fB\-q\fR
+.IP
+Proceed quietly.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+Print this help message.
+.SS tree\-building options
+.HP
+\fB\-\-tree\fR, \fB\-t\fR <tree_fname>|<tree_string>
+(Required if non\-parametric and more than two species) Name
+of file or literal string defining tree topology.
+.HP
+\fB\-\-subst\-mod\fR, \fB\-s\fR JC69|F81|HKY85|REV|SSREV|UNREST|R2|R2S|U2|U2S|R3|R3S|U3|U3S
+.TP
+(default REV).
+Nucleotide substitution model.
+.HP
+\fB\-\-nrates\fR, \fB\-k\fR <nratecats>
+(default 1).
+Number of rate categories to use. Specifying a
+.IP
+value of greater than one causes the discrete gamma model for
+rate variation to be used.
+.HP
+\fB\-\-EM\fR, \fB\-E\fR
+Use EM rather than the BFGS quasi\-Newton algorithm for parameter
+estimation.
+.HP
+\fB\-\-precision\fR, \fB\-p\fR HIGH|MED|LOW
+.IP
+(default HIGH) Level of precision to use in estimating model
+parameters.
+.HP
+\fB\-\-init\-model\fR, \fB\-M\fR <mod_fname>
+.IP
+Initialize optimization procedure with specified tree model.
+.HP
+\fB\-\-init\-random\fR, \fB\-r\fR
+.IP
+Initialize parameters randomly.
+.HP
+\fB\-\-scale\fR,\-P <rho>
+Scale input tree by factor rho before doing parametric simulations.
+.HP
+\fB\-\-subtree\fR,\-S <node>
+For use with \fB\-\-subtree\-scale\fR and/or subtree\-switch.
+Define
+.IP
+subtree including all children of named node, including branch
+leading up to node.
+.HP
+\fB\-\-subtree\-scale\fR,\-l <lambda>
+Scale subtree defined with \fB\-\-subtree\fR option by factor lambda.
+.HP
+\fB\-\-subtree\-switch\fR,\-w <prob>
+.IP
+With given probability, randomly switch branches in tree from
+subtree to supertree and vice versa. Randomization is performed
+independently for each branch in every column of simulated data.
+.HP
+\fB\-\-scale\-file\fR,\-F <file>
+(For use with \fB\-\-subtree\fR in parametric mode).
+Instead of using
+.HP
+\fB\-\-subtree\-scale\fR or \fB\-\-scale\fR, read in a tab\-delimited file with
+three columns: numSite,scale,subtree_scale.
+For each row in the
+file phyloBoot will simulate the given number of sites with those
+scaling factors, and then will move on to the next row, so that the
+total number of sites is the sum of the first column.
diff --git a/debian/help2man/phyloFit.1 b/debian/help2man/phyloFit.1
new file mode 100644
index 0000000..1d25655
--- /dev/null
+++ b/debian/help2man/phyloFit.1
@@ -0,0 +1,565 @@
+.TH PHYLOFIT "1" "May 2016" "phyloFit 1.4" "User Commands"
+.SH NAME
+phyloFit \- Fits one or more tree models to a multiple alignment of DNA
+.SH DESCRIPTION
+Fits one or more tree models to a multiple alignment of DNA
+sequences by maximum likelihood, using the specified tree topology
+and substitution model. If categories of sites are defined via
+\fB\-\-features\fR and \fB\-\-catmap\fR (see below), then a separate model will be
+estimated for each category. A description of each model will
+be written to a separate file, with the suffix ".mod". These
+\&.mod files minimally include a substitution rate matrix, a tree with
+branch lengths, and estimates of nucleotide equilibrium
+frequencies. They may also include information about parameters
+for modeling rate variation.
+.SH SYNOPSIS
+.B phyloFit
+[OPTIONS] <msa_fname>
+.PP
+<msa_fname> should be a multiple alignment in FASTA format or
+one of several alternative formats (see \fB\-\-msa\-format\fR). For
+backward compatibility, this argument may be preceded by '\-m' or
+\&'\-\-msa'. Note that \fB\-\-tree\fR is required in most cases. By default,
+all output files will have the prefix "phyloFit" (see
+\fB\-\-out\-root\fR).
+.SH EXAMPLE
+.PP
+(If you're like me, you want some basic examples first, and a list
+of all options later.)
+.PP
+1. Compute the distance between two aligned sequences (in FASTA file
+pair.fa) under the REV model.
+.IP
+phyloFit pair.fa
+.PP
+(output is to phyloFit.mod; distance in substitutions per site
+appears in the TREE line in the output file)
+.PP
+2. Fit a phylogenetic model to an alignment of human, chimp, mouse,
+and rat sequences. Use the HKY85 substitution model. Write output
+to files with prefix "myfile".
+.IP
+phyloFit \fB\-\-tree\fR "((human,chimp),(mouse,rat))" \fB\-\-subst\-mod\fR HKY85
+\fB\-\-out\-root\fR myfile primate\-rodent.fa
+.PP
+3. As above, but use the discrete\-gamma model for rate variation,
+with 4 rate categories.
+.IP
+phyloFit \fB\-\-tree\fR "((human,chimp),(mouse,rat))" \fB\-\-subst\-mod\fR HKY85
+\fB\-\-out\-root\fR myfile \fB\-\-nrates\fR 4 primate\-rodent.fa
+.PP
+4. As above, but use genome\-wide data, stored in the compact
+"sufficient\-statistics" format (can be produced with "msa_view
+\fB\-o\fR SS").
+.IP
+phyloFit \fB\-\-tree\fR "((human,chimp),(mouse,rat))" \fB\-\-subst\-mod\fR HKY85
+\fB\-\-out\-root\fR myfile \fB\-\-nrates\fR 4 \fB\-\-msa\-format\fR SS
+primate\-rodent.ss
+.PP
+5. Fit a context\-dependent phylogenetic model (U2S) to an
+alignment of human, mouse, and rat sequences. Use
+an EM algorithm for parameter optimization and relax the
+convergence criteria a bit (recommended with context\-dependent
+models). Write a log file for the optimization procedure.
+Consider only non\-overlapping pairs of sites.
+.IP
+phyloFit \fB\-\-tree\fR "(human,(mouse,rat))" \fB\-\-subst\-mod\fR U2S \fB\-\-EM\fR
+\fB\-\-precision\fR MED \fB\-\-non\-overlapping\fR \fB\-\-log\fR u2s.log \fB\-\-out\-root\fR
+hmr\-u2s hmr.fa
+.PP
+6. As above, but allow overlapping pairs of sites, and compute
+likelihoods by assuming Markov\-dependence of columns (see Siepel &
+Haussler, 2004). The EM algorithm can no longer be used
+(optimization will be much slower).
+.IP
+phyloFit \fB\-\-tree\fR "(human,(mouse,rat))" \fB\-\-subst\-mod\fR U2S
+\fB\-\-precision\fR MED \fB\-\-log\fR u2s\-markov.log \fB\-\-markov\fR hmr.fa
+.PP
+7. Compute a likelihood using parameter estimates obtained in (5)
+and an assumption of Markov dependence. This provides a lower
+bound on the likelihood of the Markov\-dependent model.
+.IP
+phyloFit \fB\-\-init\-model\fR hmr\-u2s.mod \fB\-\-lnl\fR \fB\-\-markov\fR hmr.fa
+.PP
+8. Given an alignment of several mammalian sequences (mammals.fa), a
+tree topology (tree.nh), and a set of gene annotations in GFF
+(genes.gff), fit separate models to sites in 1st, 2nd, and 3rd
+codon positions. Use the REV substitution model. Assume coding
+regions have feature type 'CDS'.
+.IP
+phyloFit \fB\-\-tree\fR tree.nh \fB\-\-features\fR genes.gff \fB\-\-out\-root\fR mammals\-rev
+\fB\-\-catmap\fR "NCATS = 3; CDS 1\-3" \fB\-\-do\-cats\fR 1,2,3 mammals.fa
+.PP
+(output will be to mammals\-rev.cds\-1.mod, mammals\-rev.cds\-2.mod, and
+mammals\-rev.cds\-3.mod)
+.SH OPTIONS
+.HP
+\fB\-\-tree\fR, \fB\-t\fR <tree_fname>|<tree_string>
+.IP
+(Required if more than three species, or more than two species
+and a non\-reversible substitution model, e.g., UNREST, U2, U3)
+Name of file or literal string defining tree topology. Tree
+must be in Newick format, with the label at each leaf equal to
+the index or name of the corresponding sequence in the alignment
+(indexing begins with 1). Examples: \fB\-\-tree\fR "(1,(2,3))",
+\fB\-\-tree\fR "(human,(mouse,rat))". Currently, the topology must be
+rooted. When a reversible substitution model is used, the root
+is ignored during the optimization procedure.
+.HP
+\fB\-\-subst\-mod\fR, \fB\-s\fR JC69|F81|HKY85|HKY85+Gap|REV|SSREV|UNREST|R2|R2S|U2|U2S|R3|R3S|U3|U3S
+.TP
+(default REV).
+Nucleotide substitution model. JC69, F81, HKY85
+.IP
+REV, and UNREST have the usual meanings (see, e.g., Yang,
+Goldman, and Friday, 1994). SSREV is a strand\-symmetric version
+of REV. HKY85+Gap is an adaptation of HKY that treats gaps as a
+fifth character (courtesy of James Taylor). The others, all
+considered "context\-dependent", are as defined in Siepel and
+Haussler, 2004. The options \fB\-\-EM\fR and \fB\-\-precision\fR MED are
+recommended with context\-dependent models (see below).
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
+(default is to guess format from file contents) Alignment format.
+FASTA is as usual. PHYLIP is compatible with the formats used in
+the PHYLIP and PAML packages. MPM is the format used by the
+MultiPipMaker aligner and some other of Webb Miller's older tools.
+MAF ("Multiple Alignment Format") is used by MULTIZ/TBA and the
+UCSC Genome Browser. SS is a simple format describing the
+sufficient statistics for phylogenetic inference (distinct columns
+or tuple of columns and their counts). Note that the program
+"msa_view" can be used for file conversion.
+.HP
+\fB\-\-out\-root\fR, \fB\-o\fR <output_fname_root>
+(default "phyloFit").
+Use specified string as root filename
+for all files created.
+.HP
+\fB\-\-min\-informative\fR, \fB\-I\fR <ninf_sites>
+.IP
+Require at least <ninf_sites> "informative" sites \fB\-\-\fR i.e.,
+sites at which at least two non\-gap and non\-missing\-data ('N'
+or '*') characters are present. Default is 50.
+.HP
+\fB\-\-gaps\-as\-bases\fR, \fB\-G\fR
+Treat alignment gap characters ('\-') like ordinary bases.
+By
+.IP
+default, they are treated as missing data.
+.HP
+\fB\-\-ignore\-branches\fR, \fB\-b\fR <branches>
+.IP
+Ignore specified branches in likelihood computations and parameter
+estimation, and treat the induced subtrees as independent. Can be
+useful for likelihood ratio tests. The argument <branches> should
+be a comma\-separated list of nodes in the tree, indicating the
+branches above these nodes, e.g., human\-chimp,cow\-dog. (See
+tree_doctor \fB\-\-name\-ancestors\fR regarding names for ancestral nodes.)
+This option does not currently work with \fB\-\-EM\fR.
+.HP
+\fB\-\-quiet\fR, \fB\-q\fR
+Proceed quietly.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
+(Options for controlling and monitoring the optimization procedure)
+.HP
+\fB\-\-lnl\fR, \fB\-L\fR
+.IP
+(for use with \fB\-\-init\-model\fR) Simply evaluate the log likelihood of
+the specified tree model, without performing any further
+optimization. Can be used with \fB\-\-post\-probs\fR, \fB\-\-expected\-subs\fR, and
+\fB\-\-expected\-total\-subs\fR.
+.HP
+\fB\-\-EM\fR, \fB\-E\fR
+.IP
+Fit model(s) using EM rather than the BFGS quasi\-Newton
+algorithm (the default).
+.HP
+\fB\-\-precision\fR, \fB\-p\fR HIGH|MED|LOW
+.IP
+(default HIGH) Level of precision to use in estimating model
+parameters. Affects convergence criteria for iterative
+algorithms: higher precision means more iterations and longer
+execution time.
+.HP
+\fB\-\-log\fR, \fB\-l\fR <log_fname>
+.IP
+Write log to <log_fname> describing details of the optimization
+procedure.
+.HP
+\fB\-\-init\-model\fR, \fB\-M\fR <mod_fname>
+Initialize with specified tree model.
+By choosing good
+.IP
+starting values for parameters, it is possible to reduce
+execution time dramatically. If this option is chosen, \fB\-\-tree\fR
+is not allowed. The substitution model used in the given
+model will be used unless \fB\-\-subst\-mod\fR is also specified.
+Note: currently only one mod_fname may be specified; it will be
+used for all categories.
+.HP
+\fB\-\-init\-random\fR, \fB\-r\fR
+Initialize parameters randomly.
+Can be used multiple times to test
+.IP
+whether the m.l.e. is real.
+.HP
+\fB\-\-seed\fR, \fB\-D\fR <seed>
+.IP
+Provide a random number seed for choosing initial parameter values
+(usually with \fB\-\-init\-random\fR, though random values are used in some
+other cases as well). Should be an integer >=1. If not provided,
+seed is chosen based on current time.
+.HP
+\fB\-\-init\-parsimony\fR, \fB\-y\fR
+Initialize branch lengths using parsimony counts for given data.
+Only currently implemented for models with single character state
+(ie, not di\- or tri\-nucleotides). Other \fB\-\-init\fR options such
+as \fB\-\-init\-random\fR or \fB\-\-init\-model\fR can be used in conjunction to
+initialize substitution matrix parameters.
+.HP
+\fB\-\-print\-parsimony\fR, \fB\-Y\fR <filename>
+.TP
+Print parsimony score to given file, and quit.
+(Does not optimize
+.IP
+or report likelihoods).
+.HP
+\fB\-\-clock\fR, \fB\-z\fR
+Assume a molecular clock in estimation.
+Causes the distances to all
+descendant leaves to be equal for each ancestral node and cuts the
+number of free branch\-length parameters roughly in half.
+.HP
+\fB\-\-scale\-only\fR, \fB\-B\fR
+.IP
+(for use with \fB\-\-init\-model\fR) Estimate only the scale of the tree,
+rather than individual branch lengths (branch proportions fixed).
+Equilibrium frequencies and rate\-matrix parameters will still be
+estimated unless \fB\-\-no\-freqs\fR and \fB\-\-no\-rates\fR are used.
+.HP
+\fB\-\-scale\-subtree\fR, \fB\-S\fR <node_name>
+(for use with \fB\-\-scale\-only\fR) Estimate separate scale factors for
+subtree beneath identified node and rest of tree. The branch
+leading to the subtree is included with the subtree. If ":loss" or
+":gain" is appended to <node_name>, subtree scale is constrained to
+be greater than or less than (respectively) scale for rest of tree.
+.HP
+\fB\-\-estimate\-freqs\fR, \fB\-F\fR
+.IP
+Estimate equilibrium frequencies by maximum likelihood, rather
+than approximating them by the relative frequencies in the data.
+If using the SSREV model, this option implies \fB\-\-sym\-freqs\fR.
+.HP
+\fB\-\-sym\-freqs\fR, \fB\-W\fR
+.IP
+Estimate equilibrium frequencies, assuming freq(A)=freq(T) and
+freq(C)=freq(G). This only works for an alphabet ACGT (and possibly
+gap). This option implies \fB\-\-estimate\-freqs\fR.
+.HP
+\fB\-\-no\-freqs\fR, \fB\-f\fR
+.IP
+(for use with \fB\-\-init\-model\fR) Do not estimate equilibrium
+frequencies; just use the ones from the given tree model.
+.HP
+\fB\-\-no\-rates\fR, \fB\-n\fR
+.IP
+(for use with \fB\-\-init\-model\fR) Do not estimate rate\-matrix
+parameters; just use the ones from the given tree model.
+.HP
+\fB\-\-ancestor\fR, \fB\-A\fR <seqname>
+Treat specified sequence as the root of the tree.
+The tree
+topology must define this sequence to be a child of the root
+(in practice, the branch from the root to the specified
+sequence will be retained, but will be constrained to have
+length zero).
+.HP
+\fB\-\-error\fR, \fB\-e\fR <filename>
+.IP
+For each parameter, report estimate, variance, and 95%% confidence
+interval, printed to given filename, one parameter per line.
+.HP
+\fB\-\-no\-opt\fR, \fB\-O\fR <param_list>
+Hold parameters listed in comma\-separated param_list constant at
+initial values. This applies only to the "main" model, and not to
+any models defined with the \fB\-\-alt\-mod\fR option. Param list can
+contain values such as "branches" to hold branch lengths constant,
+"ratematrix", "backgd", or "ratevar" to hold entire rate matrix,
+equilibrium frequencies, or rate variation parameters constant
+(respectively). There are also substitution model\-specific
+parameters such as "kappa" (transition/transversion rate ratio).
+Note: to hold certain branches constant, but optimize others,
+put an exclamation point in the newick\-formatted tree after the
+branch lengths that should be held constant. This can be useful
+for enforcing a star\-phylogeny. However, note that the two branches
+coming from root of tree are treated as one. So they should both
+be held constant, or not held constant. This option does *not* work
+with \fB\-\-scale\-only\fR or \fB\-\-clock\fR.
+.HP
+\fB\-\-bound\fR <param_name[lower_bound,upper_bound]>
+Set boundaries for parameter.
+lower_bound or upper_bound may be
+empty string to keep default.
+For example \fB\-\-bound\fR gc_param[1,] will
+.IP
+set the lower bound for gc_param to 1 (keeping upper bound at infinity),
+for a GC model. Only applies to parameters for model in the "main"
+tree, but similar syntax can be used within the \fB\-\-alt\-mod\fR arguments.
+Can be used multiple times to set boundaries for different parameters.
+.HP
+\fB\-\-selection\fR <selection_param>
+.IP
+Use selection in the model (is also implied if \fB\-\-init\-model\fR is used
+and contains selection parameter). Selection scales rate matrix
+entries by selection_param/(1\-exp(\fB\-selection\-param\fR)); this is done
+after rate matrix is scaled to set expected number of substitutions
+per unit time to 1. If using codon models selection acts only on
+nonysynonymous mutations.
+(Options for modeling rate variation)
+.HP
+\fB\-\-nrates\fR, \fB\-k\fR <nratecats>
+(default 1).
+Number of rate categories to use. Specifying a
+.IP
+value of greater than one causes the discrete gamma model for
+rate variation to be used (Yang, 1994).
+.HP
+\fB\-\-alpha\fR, \fB\-a\fR <alpha>
+(for use with \fB\-\-nrates\fR).
+Initial value for alpha, the shape
+parameter of the gamma distribution.
+Default is 1.
+.HP
+\fB\-\-rate\-constants\fR, \fB\-K\fR <rate_consts>
+.IP
+Use a non\-parameteric mixture model for rates, instead of
+assuming a gamma distribution. The argument <rate_consts>
+must be a comma\-delimited list explicitly defining the rate
+constants to be used. The "weight" (mixing proportion)
+associated with each rate constant will be estimated by EM
+(this option implies \fB\-\-EM\fR). If \fB\-\-alpha\fR is used with
+this option, then the mixing proportions will be initialized
+to reflect a gamma distribution with the specified shape
+parameter.
+(Options for separate handling of sites in different annotation categories)
+.HP
+\fB\-\-features\fR, \fB\-g\fR <fname>
+.IP
+Annotations file (GFF or BED format) describing features on
+one or more sequences in the alignment. Together with a
+category map (see \fB\-\-catmap\fR), will be taken to define site
+categories, and a separate model will be estimated for each
+category. If no category map is specified, a category will be
+assumed for each type of feature, and they will be numbered in
+the order of appearance of the features. Features are assumed
+to use the coordinate frame of the first sequence in the
+alignment and should be non\-overlapping (see 'refeature
+\fB\-\-unique\fR').
+.HP
+\fB\-\-catmap\fR, \fB\-c\fR <fname>|<string>
+.IP
+(optionally use with \fB\-\-features\fR) Mapping of feature types to
+category numbers. Can either give a filename or an "inline"
+description of a simple category map, e.g., \fB\-\-catmap\fR "NCATS =
+3 ; CDS 1\-3" or \fB\-\-catmap\fR "NCATS = 1 ; UTR 1". Note that
+category 0 is reserved for "background" (everything that is
+not described by a defined feature type).
+.HP
+\fB\-\-do\-cats\fR, \fB\-C\fR <cat_list>
+.IP
+(optionally use with \fB\-\-features\fR) Estimate models for only the
+specified categories (comma\-delimited list categories, by name
+or numbera). Default is to fit a model for every category.
+.HP
+\fB\-\-reverse\-groups\fR, \fB\-R\fR <tag>
+.IP
+(optionally use with \fB\-\-features\fR) Group features by <tag> (e.g.,
+"transcript_id" or "exon_id") and reverse complement
+segments of the alignment corresponding to groups on the
+reverse strand. Groups must be non\-overlapping (see refeature
+\fB\-\-unique\fR). Useful with categories corresponding to
+strand\-specific phenomena (e.g., codon positions).
+(Options for context\-dependent substitution models)
+.HP
+\fB\-\-markov\fR, \fB\-N\fR
+.IP
+(for use with context\-dependent substitutions models and not
+available with \fB\-\-EM\fR.) Assume Markov dependence of alignment
+columns, and compute the conditional probability of each
+column given its N\-1 predecessors using the two\-pass algorithm
+described by Siepel and Haussler (2004). (Here, N is the
+"order" of the model, as defined by \fB\-\-subst\-mod\fR; e.g., N=1
+for REV, N=2 for U2S, N=3 for U3S.) The alternative (the
+default) is simply to work with joint probabilities of tuples
+of columns. (You can ensure that these tuples are
+non\-overlapping with the \fB\-\-non\-overlapping\fR option.) The use
+of joint probabilities during parameter estimation allows the
+use of the \fB\-\-EM\fR option and can be much faster; in addition, it
+appears to produce nearly equivalent estimates. If desired,
+parameters can be estimated without \fB\-\-markov\fR, and
+then the likelihood can be evaluated using \fB\-\-lnl\fR and
+\fB\-\-markov\fR together. This gives a lower bound on the
+likelihood of the Markov\-dependent model.
+.HP
+\fB\-\-non\-overlapping\fR, \fB\-V\fR
+(for use with context\-dependent substitution models; not
+compatible with \fB\-\-markov\fR, \fB\-\-features\fR, or
+\fB\-\-msa\-format\fR SS) Avoid using overlapping tuples of sites
+in parameter estimation. If a dinucleotide model is selected,
+every other tuple will be considered, and if a nucleotide
+triplet model is selected, every third tuple will be
+considered. This option cannot be used with an alignment
+represented only by unordered sufficient statistics.
+(Option for lineage\-specific models)
+.HP
+\fB\-\-label\-branches\fR branch1,branch2,branch3...:label
+.IP
+Create a group of branches by giving a set of branches a
+single label. The label should be a word which does not
+contain special characters (in particular, no spaces, brackets,
+parentheses, pound signs, commas, or colons).
+The label is for use with \fB\-\-alt\-model\fR option below, so that an
+alternate model can be defined for a set of branches. A branch
+is specified by the name of the node which is a descendant of
+that branch.
+.IP
+For example,
+\fB\-\-label\-branches\fR hg18,chimp,hg18\-chimp:HC
+will apply the label "HC" to the hg18,chimp,and hg18\-chimp
+branches in the following tree:
+(((hg18,chimp)hg18\-chimp, (mouse,rat)mouse\-rat)
+.IP
+The same label could be defined without using \fB\-\-label\-branches\fR
+by specifying the tree (either on the command\-line or within
+init\-model) as follows:
+(((hg18 # HC, chimp #HC)#HC, (mouse,rat))
+.HP
+\fB\-\-label\-subtree\fR node[+]:label
+Similar to label\-branches, except labels the entire subtree
+of the named node. If the node name is followed by a "+" sign,
+then includes the branch leading up to the node in the subtree.
+.HP
+\fB\-\-alt\-model\fR, \fB\-d\fR <label:(model|param_list)>
+Create a lineage\-specific substitution model on a group of branches.
+The group is defined by a label, which can be specified within
+the tree string (using the # sign notation), or by using the
+\fB\-\-label\-branches\fR or \fB\-\-label\-subtree\fR arguments. If the alt\-model
+applies to only a single branch, labelling is not necessary and
+the name of the node descending from the branch can be used instead.
+See \fB\-\-label\-branches\fR above for more details on labelling groups of
+branches.
+If a name of a substitution model (HKY85, REV, UNREST, etc)
+is given after the colon, then this model will be used for the
+group of branches, and parameters relevant to the model will be
+estimated separately in this group. This model may be different
+(or the same) as the model used in the rest of the tree, but it
+must have the same number of states and be of the same order as
+the model used for the rest of the tree.
+.IP
+Alternately, a list of parameter names can be given after the colon.
+In this case, the same substitution model will be used for the
+entire tree, but the parameters listed will be estimated separately
+in the specified group of branches.
+.IP
+The parameter names are model\-specific, and include "kappa" for
+HKY models, "alpha" for GC models, "ratematrix" to specify
+all rate\-matrix parameters in general models, and "backgd" for
+the equilibrium background frequencies. The parameter names
+may optionally be followed by boundaries in square brackets to
+specify parameter bounds, as described in \fB\-\-bound\fR option.
+.IP
+The \fB\-\-alt\-model\fR argument may be used multiple times, if one
+wishes to (for example) optimize a parameter independently
+on several different groups of branches.
+Example:
+phyloFit align.fa \fB\-\-subst\-mod\fR HKY85 \e
+\fB\-\-tree\fR "(human, (mouse#MR, rat#MR)#MR, cow)"\e
+\fB\-\-alt\-model\fR "MR:kappa[0, 1]"
+.IP
+will estimate the HKY85 parameter kappa separately on the
+mouse/rat subtree, and constrain kappa between 0 and 1. The
+quotes are often necessary to prevent the square brakcets from
+being parsed by the shell. The same model could be achieved with:
+.IP
+phyloFit align.fa \fB\-\-subst\-mod\fR HKY85 \e
+\fB\-\-tree\fR "(human, (mouse,rat)mouse\-rat, cow)"\e
+\fB\-\-label\-branches\fR mouse,rat,mouse\-rat:MR \e
+\fB\-\-alt\-model\fR "MR:kappa[0,1]"
+or
+.IP
+phyloFit align.fa \fB\-\-subst\-mod\fR HKY85 \e
+\fB\-\-tree\fR "(human, (mouse,rat)mouse\-rat, cow)" \e
+\fB\-\-label\-subtree\fR "mouse\-rat+:MR" \e
+\fB\-\-alt\-model\fR "MR:kappa[0,1]"
+.IP
+(Options for posterior probabilities)
+.HP
+\fB\-\-post\-probs\fR, \fB\-P\fR
+.IP
+Output posterior probabilities of all bases at all ancestral
+nodes. Output will be to auxiliary file(s) with suffix
+".postprobs".
+.HP
+\fB\-\-expected\-subs\fR, \fB\-X\fR
+.IP
+Output posterior expected number of substitutions on each branch at
+each site, summed across all types of substitutions.
+Output will be to auxiliary file(s) with suffix ".expsub".
+.HP
+\fB\-\-expected\-subs\-col\fR, \fB\-J\fR
+.IP
+Output posterior expected number of substitutions of each type
+on each branch, for each site. Output will be to auxiliary
+file(s) with suffix .expcolsub
+.HP
+\fB\-\-expected\-total\-subs\fR, \fB\-Z\fR
+.IP
+Output posterior expected number of substitutions of each type
+on each branch, summed across all sites. Output will be to
+auxiliary file(s) with suffix ".exptotsub".
+.HP
+\fB\-\-column\-probs\fR, \fB\-U\fR
+.TP
+(for use with \fB\-init\-model\fR; implies \fB\-\-lnl\fR)
+Output a separate log
+.TP
+probability for each type of column in the input.
+Output will
+.TP
+be to a file with suffix ".colprobs".
+Values are log base 2.
+.IP
+(Options for estimation in sliding window)
+.HP
+\fB\-\-windows\fR, \fB\-w\fR <size,shift>
+Apply a sliding window to the alignment, and fit a separate
+tree to each window. Arguments specify size of window and
+amount by which to shift it on each iteration, both in bases
+of the first sequence in the alignment (assumed to be the
+reference sequence). Separate versions of all output files
+will be created for each window.
+.HP
+\fB\-\-windows\-explicit\fR, \fB\-v\fR <window_coord_list>
+Like \fB\-\-windows\fR, except that all start and end coordinates must
+be explicitly specified. Each successive pair of numbers is
+interpreted as defining the start and end of a window. Can be
+used with a two\-column file and the '*' operator, e.g.,
+\fB\-\-windows\-explicit\fR '*mycoords'.
+.SH SEE ALSO
+.TP
+A. Siepel and D. Haussler.
+2004. Phylogenetic estimation of
+context\-dependent substitution rates by maximum likelihood.
+Mol. Biol. Evol., 21:468\-488.
+.TP
+Z. Yang, N. Goldman, and A. Friday.
+1994. Comparison of models for
+nucleotide substution used in maximum likelihood phylogenetic
+estimation. Mol. Biol. Evol., 11:316\-324.
+.TP
+Z. Yang. 1994. Maximum likelihood phylogenetic estimation from
+DNA sequences with variable rates over sites: approximate
+methods. J. Mol. Evol., 39:306\-314.
diff --git a/debian/help2man/phyloP.1 b/debian/help2man/phyloP.1
new file mode 100644
index 0000000..d520f0d
--- /dev/null
+++ b/debian/help2man/phyloP.1
@@ -0,0 +1,305 @@
+.TH PHYLOP "1" "May 2016" "phyloP 1.4" "User Commands"
+.SH NAME
+phyloP \- Compute conservation or acceleration p-values based on an alignment and
+The phylogenetic model must be in the .mod format produced by the
+phyloFit program. The alignment file can be in any of several file
+formats (see \fB\-\-msa\-format\fR). No alignment is required with the \fB\-\-null\fR
+option.
+.SH DESCRIPTION
+Compute conservation or acceleration p\-values based on an alignment and
+a model of neutral evolution. Will also compute p\-values of
+conservation/acceleration in a subtree and in its complementary
+supertree given the whole tree (see \fB\-\-subtree\fR). P\-values can be
+produced for entire input alignments (the default), pre\-specified
+intervals within an alignment (see \fB\-\-features\fR), or individual sites
+(see \fB\-\-wig\-scores\fR and \fB\-\-base\-by\-base\fR).
+.PP
+The default behavior is to compute a null distribution for the total
+number of substitutions from the tree model, an estimate of the number
+of substitutions that have actually occurred, and the p\-value of this
+estimate wrt the null distribution. These computations are performed
+as described by Siepel, Pollard, and Haussler (2006). In addition to
+the SPH method, phyloP can compute p\-values or
+conservation/acceleration scores using a likelihood ratio test
+(\fB\-\-method\fR LRT), a score\-based test (\fB\-\-method\fR SCORE), or a procedure
+similar to that used by GERP (Cooper et al., 2005) (\fB\-\-method\fR GERP).
+These alternative methods are currently supported only with
+\fB\-\-base\-by\-base\fR, \fB\-\-wig\-scores\fR, or \fB\-\-features\fR.
+.PP
+The main advantage of the SPH method is that it can provide a complete
+and exact description of distributions over numbers of substitutions.
+However, simulation experiments suggest that the LRT and SCORE methods
+have somewhat better power than SPH for identifying selection,
+especially when the expected number of substitutions is small (e.g.,
+with short branch lengths and/or short intervals/individual sites).
+These two methods are also faster. They are generally similar to one
+another in power, but in many cases SCORE is considerably faster than
+LRT. On the other hand, SCORE appears to have slightly less power than
+LRT at low false positive rates, i.e., for cases of extreme selection.
+Thus, when using \fB\-\-base\-by\-base\fR, \fB\-\-wig\-scores\fR, or \fB\-\-features\fR, LRT is
+recommended for most purposes, but SCORE is a good alternative if speed
+is an issue.
+When computing p\-values with the SPH method, the default is to use the
+posterior expected number of substitutions as an estimate of the actual
+number. This is a conservative estimate, because it is biased toward
+the mean of the null distribution by the prior. These p\-values can be
+made less conservative with \fB\-\-fit\-model\fR and more conservative with
+\fB\-\-confidence\-interval\fR (see below).
+.SH EXAMPLE
+.PP
+1. Using the SPH method, compute and report p\-values of conservation
+and acceleration for a given alignment with respect to a neutral model
+of evolution. Estimated numbers of substitutions are also reported.
+.IP
+phyloP neutral.mod alignment.fa > report.txt
+.PP
+The file neutral.mod could be produced by running phyloFit on data from
+ancestral repeats or fourfold degenerate sites with an appropriate tree
+topology and substitution model.
+.PP
+2. Compute and report p\-values of conservation and acceleration for a
+particular subtree of interest (using SPH).
+.IP
+phyloP \fB\-\-subtree\fR human\-mouse_lemur neutral.mod alignment.fa > report.txt
+.PP
+Here human\-mouse_lemur denote the most recent common ancestor of human
+and mouse_lemur, which is the node that defines the primate clade in
+this phylogeny. The tree_doctor program with the \fB\-\-name\-ancestors\fR
+option can be used to assign names to ancestral nodes of the tree.
+.PP
+3. Describe the complete null distribution over the number of
+substitutions for a 10bp alignment given the specified neutral model
+(using SPH).
+.IP
+phyloP \fB\-\-null\fR 10 neutral.mod > null.txt
+.PP
+A two\-column table is produced with numbers of substitutions and their
+probabilities, up to an appropriate upper limit.
+.PP
+4. Describe the complete posterior distribution over the number of
+substitutions in a given alignment (using SPH).
+.IP
+phyloP \fB\-\-posterior\fR neutral.mod alignment.fa > posterior.txt
+.PP
+5. Compute conservation scores (\fB\-log10\fR p\-values) for each site in an
+alignment and output them in the fixed\-step wig format (see
+http://genome.ucsc.edu/goldenPath/help/wiggle.html). Use the
+likelihood ratio test (LRT) method.
+.IP
+phyloP \fB\-\-wig\-scores\fR \fB\-\-method\fR LRT neutral.mod alignment.fa > scores.wig
+.PP
+The \fB\-\-mode\fR option can be used instead to produce acceleration scores
+(ACC), scores of nonneutrality (NNEUT), or scores that summarize
+conservation and acceleration (CONACC). The \fB\-\-base\-by\-base\fR option can
+be used to output additional statistics of interest (estimated scale
+factors, log10 likelihood ratios, etc.). As discussed above, several
+arguments to \fB\-\-method\fR are possible.
+.PP
+6. Similarly, compute scores describing lineage\-specific conservation
+in primates.
+.IP
+phyloP \fB\-\-wig\-scores\fR \fB\-\-method\fR LRT \fB\-\-subtree\fR human\-mouse_lemur
+neutral.mod alignment.fa > scores.wig
+.PP
+7. Compute conservation p\-values and associated statistics for each
+element in a BED file. This time use a score test and allow for
+acceleration as well as conservation, flagging elements under
+acceleration by making their p\-values negative (CONACC mode).
+.IP
+phyloP \fB\-\-features\fR elements.bed \fB\-\-method\fR SCORE \fB\-\-mode\fR CONACC
+neutral.mod alignment.fa > element\-scores.txt
+.PP
+This option can also be used with \fB\-\-subtree\fR.
+The \fB\-\-gff\-scores\fR option
+can be used to output the original features in GFF format with scores
+equal to \fB\-log10\fR p. Note that the input file can be in GFF instead of BED
+format.
+.SH OPTIONS
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
+.IP
+Alignment format (default is to guess format from file contents).
+.HP
+\fB\-\-method\fR, \fB\-m\fR SPH|LRT|SCORE|GERP
+.IP
+Method used to compute p\-values or conservation/acceleration scores
+(Default SPH). The likelihood ratio test (LRT) and score test
+(SCORE) compare an alternative model having a free scale parameter
+with the given neutral model, or, if \fB\-\-subtree\fR is used, an
+alternative model having free scale parameters for the supertree
+and subtree with a null model having a single free scale parameter.
+P\-values are computed by comparing test statistics with asymptotic
+chi\-square null distributions. The GERP\-like method (GERP)
+estimates the number of "rejected substitutions" per base by
+comparing the (per\-site) maximum likelihood expected number of
+substitutions with the expected number under the neutral model.
+Currently LRT, SCORE, and GERP can be used only with
+\fB\-\-base\-by\-base\fR, \fB\-\-wig\-scores\fR, or \fB\-\-features\fR.
+.HP
+\fB\-\-wig\-scores\fR, \fB\-w\fR
+.IP
+Compute separate p\-values per site, and then compute site\-specific
+conservation (acceleration) scores as \fB\-log10\fR(p). Output base\-by\-base
+scores in fixed\-step wig format, using the coordinate system of the
+reference sequence (see \fB\-\-refidx\fR). In GERP mode, outputs rejected
+substitutions per site instead of \fB\-log10\fR p\-values.
+.HP
+\fB\-\-base\-by\-base\fR, \fB\-b\fR
+.IP
+Like \fB\-\-wig\-scores\fR, but outputs multiple values per site, in a
+method\-dependent way. With 'SPH', output includes mean and
+variance of posterior distribution, with LRT and SCORE it
+includes the estimated scale factor(s) and test statistics, and
+with GERP it includes the estimated numbers of neutral,
+observed, and rejected substitutions, along with the number of
+species available at each site.
+.HP
+\fB\-\-refidx\fR, \fB\-r\fR <refseq_idx>
+.IP
+(for use with \fB\-\-wig\-scores\fR or \fB\-\-base\-by\-base\fR) Use coordinate frame
+of specified sequence in output. Default value is 1, first
+sequence in alignment; 0 indicates coordinate frame of entire
+multiple alignment.
+.HP
+\fB\-\-mode\fR, \fB\-o\fR CON|ACC|NNEUT|CONACC
+.IP
+(For use with \fB\-\-wig\-scores\fR, \fB\-\-base\-by\-base\fR, or \fB\-\-features\fR) Whether
+to compute one\-sided p\-values so that small p (large \fB\-log10\fR p)
+indicates unexpected conservation (CON; the default) or
+acceleration (ACC); or two\-sided p\-values such that small p
+indicates an unexpected departure from neutrality (NNEUT). The
+fourth option (CONACC) uses positive values (p\-values or scores) to
+indicate conservation and negative values to indicate acceleration.
+In GERP mode, CON and CONACC both report the number of rejected
+substitutions R (which may be negative), while ACC reports \fB\-R\fR, and
+NNEUT reports abs(R).
+.HP
+\fB\-\-features\fR, \fB\-f\fR <file>
+.IP
+Read features from <file> (GFF or BED format) and output a
+table of p\-values and related statistics with one row per
+feature. The features are assumed to use the coordinate frame
+of the first sequence in the alignment. Not for use with
+\fB\-\-null\fR or \fB\-\-posterior\fR. See also \fB\-\-gff\-scores\fR.
+.HP
+\fB\-\-gff\-scores\fR, \fB\-g\fR
+.IP
+(For use with features)
+Instead of a table, output a GFF and
+assign each feature a score equal to its \fB\-log10\fR p\-value.
+.HP
+\fB\-\-subtree\fR, \fB\-s\fR <node\-name>
+.IP
+(Not available in GERP mode) Partition the tree into the subtree
+beneath the node whose name is given and the complementary
+supertree, and consider conservation/acceleration in the subtree
+given the supertree. The branch above the specified node is
+included with the subtree. Thus, given the tree
+"((human,chimp)primate,(mouse,rat)rodent)", the option "\-\-subtree
+primate" will create one partition consisting of human, chimp, and
+the branch leading to them, and another partition consisting of the
+rest of the tree; "\-\-subtree human" will create one partition
+consisting only of human and the branch leading to it and another
+partition consisting of the rest of the tree. In 'SPH' mode, a
+reversible substitution model is assumed.
+.HP
+\fB\-\-branch\fR, \fB\-B\fR <node\-name(s)>
+.IP
+(Not available in GERP or SPH mode).
+Like subtree, but partitions
+the tree into the set of named branches (each named by its child
+node), and all the remaining branches. Then tests for conservation/
+acceleration in the set of named branches relative to the others.
+The argument is a comma\-delimited list of child nodes.
+.HP
+\fB\-\-chrom\fR, \fB\-N\fR <name>
+.IP
+(Optionally use with \fB\-\-wig\-scores\fR or \fB\-\-base\-by\-base\fR) Chromosome
+name for wig output. Default is root of multiple alignment
+filename.
+.HP
+\fB\-\-log\fR, \fB\-l\fR <fname>
+.IP
+Write log to <fname> describing details of parameter optimization.
+Useful for debugging. (Warning: may produce large file.)
+.HP
+\fB\-\-seed\fR, \fB\-d\fR <seed>
+.IP
+Provide a random number seed, should be an integer >=1.
+Random numbers are used in some cases to generate starting values for
+optimization. If not specified will use a seed based on the
+current time.
+.HP
+\fB\-\-no\-prune\fR,\-P
+.IP
+Do not prune species from tree which are not in alignment.
+Rather,
+treat these species as having missing data in the alignment.
+Missing
+data does have an effect on the results when \fB\-\-method\fR SPH is used.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Produce this help message.
+.SS Options for SPH mode only
+.HP
+\fB\-\-null\fR, \fB\-n\fR <nsites>
+Compute just the null (prior) distribution of the number of
+substitutions, as defined by the tree model and the given
+number of sites, and output as a table. The 'alignment'
+argument will be ignored. If used with \fB\-\-subtree\fR, the joint
+distribution over the number of substitutions in the specified
+supertree and subtree will be output instead.
+.HP
+\fB\-\-posterior\fR, \fB\-p\fR
+Compute just the posterior distribution of the number of
+substitutions, given the alignment and the model, and output
+as a table. If used with \fB\-\-subtree\fR, the joint distribution
+over the number of substitutions in the specified supertree
+and subtree will be output instead.
+.HP
+\fB\-\-fit\-model\fR, \fB\-F\fR
+.IP
+Fit model to data before computing posterior distribution, by
+estimating a scale factor for the whole tree or (if \fB\-\-subtree\fR)
+separate scale factors for the specified subtree and supertree.
+Makes p\-values less conservative. This option has no effect with
+\fB\-\-null\fR and currently cannot be used with \fB\-\-features\fR. It can be
+used with \fB\-\-wig\-scores\fR and \fB\-\-base\-by\-base\fR.
+.HP
+\fB\-\-epsilon\fR, \fB\-e\fR <val>
+.IP
+(Default 1e\-10 or 1e\-6 if \fB\-\-wig\-scores\fR or \fB\-\-base\-by\-base\fR) Threshold
+used in truncating tails of distributions; tail probabilities less
+than this value are discarded. To get accurate p\-values smaller
+than 1e\-10, this option will need to be used, at some cost in
+speed. Note that truncation affects only *right* tails, not left
+tails, so it should be an issue only with p\-values of acceleration.
+.HP
+\fB\-\-confidence\-interval\fR, \fB\-c\fR <val>
+.IP
+Allow for uncertainty in the estimate of the actual number of
+substitutions by using a (central) confidence interval about the
+mean of the specified size (0 < val < 1). To be conservative, the
+maximum of this interval is used when computing a p\-value of
+conservation, and the minimum is used when computing a p\-value of
+acceleration. The variance of the posterior is computed
+exactly, but the confidence interval is based on the assumption
+that the combined distribution will be approximately normal (true
+for large numbers of sites by central limit theorem).
+.HP
+\fB\-\-quantiles\fR, \fB\-q\fR
+.IP
+(For use with \fB\-\-null\fR or \fB\-\-posterior\fR) Report quantiles of
+distribution rather than whole distribution.
+.SH SEE ALSO
+.PP
+Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program,
+Green ED, Batzoglou S, Sidow A. Distribution and intensity of
+constraint in mammalian genomic sequence. Genome Res. 2005
+15(7):901\-13.
+.PP
+Siepel A, Pollard KS, and Haussler D. New methods for detecting
+lineage\-specific selection. In Proceedings of the 10th International
+Conference on Research in Computational Molecular Biology (RECOMB
+2006), pp. 190\-205.
diff --git a/debian/help2man/prequel.1 b/debian/help2man/prequel.1
new file mode 100644
index 0000000..a975852
--- /dev/null
+++ b/debian/help2man/prequel.1
@@ -0,0 +1,201 @@
+.TH PREQUEL "1" "May 2016" "prequel 1.4" "User Commands"
+.SH NAME
+prequel \- Compute marginal probability distributions for bases at ancestral
+.SH DESCRIPTION
+Compute marginal probability distributions for bases at ancestral
+nodes in a phylogenetic tree, using the tree model defined in
+tree.mod (may be produced with phyloFit). These distributions
+are computed using the sum\-product algorithm, assuming
+independence of sites.
+.PP
+Currently, indels are not treated probabilistically (hence the
+"largely") but are reconstructed by parsimony, also assuming site
+independence. Specifically, each base is assumed to have been inserted
+on the branch leading to the last common ancestor (LCA) of all species
+that have actual bases (as opposed to alignment gaps or missing data)
+at a given site; gaps in descendant species are assumed to have arisen
+(parsimoniously) from deletions. When this LCA is either the left or
+right child of the root, insertions on one branch cannot be
+distinguished from deletions on the other. We conservatively assume
+that the base was present at the root and was subsequently deleted.
+(Note that this will produce an upward bias on the length of the
+sequence at the root.)
+Output is to files of the form outroot.XXX.probs, where XXX is the
+name of an ancestral node in the tree. These nodes may be named
+explicitly in tree.mod. Any ancestral node that is left unnamed
+will be given a name that is a concatenation of two names,
+belonging to arbitrarily selected leaves of each subtree beneath
+the node (see below).
+.SH EXAMPLE
+.PP
+Given a multiple alignment in a file called "mammals.fa" and a
+tree model called "mytree.mod" (see phyloFit), reconstruct all
+ancestral sequences:
+.IP
+prequel mammals.fa mytree.mod anc
+.PP
+If the TREE definition in mytree.mod has labeled ancestral nodes,
+e.g.,
+.IP
+TREE: ((human:0.101627,chimp:0.149870)primate:0.035401,(mouse:0.280291,rat:0.157212)rodent:0.035401)mammal;
+.PP
+then output will be to files named "anc.primate.probs",
+"anc.rodent.probs", and "anc.mammal.probs". (See
+http://evolution.genetics.washington.edu/phylip/newicktree.html)
+If instead the ancestral nodes are unlabeled, e.g.,
+.IP
+TREE: ((human:0.101627,chimp:0.149870):0.035401,(mouse:0.280291,rat:0.157212):0.035401);
+.PP
+then names will be created by concatenating leaf names, e.g.,
+"anc.human\-chimp.probs", "anc.mouse\-rat.probs", and
+"anc.human\-mouse.probs".
+.PP
+Each output file will consist of a row for each position in the
+sequence and a column for each base, with the (i,j)th value giving
+the probability of base j at position i. For example,
+.IP
+#p(A)
+.IP
+p(C) p(G) p(T)
+.IP
+0.001449
+.IP
+0.000039 0.998460 0.000052
+.IP
+0.998150
+.IP
+0.000065 0.001755 0.000030
+.IP
+0.000427
+.IP
+0.271307 0.000599 0.727668
+.IP
+0.001449
+.IP
+0.000039 0.998460 0.000052
+.IP
+0.025826
+.IP
+0.000179 0.973813 0.000182
+.IP
+\&...
+.PP
+By default, no row is reported for bases inferred not to have been
+present at an ancestral node, so the number of rows will generally
+be smaller than the number of columns in the input alignment.
+However, if you wish to maintain a correspondence between row
+number and alignment column, you can use the \fB\-\-keep\-gaps\fR option,
+which will cause "padding" rows to be included in the output,
+e.g.,
+.IP
+#p(A)
+.IP
+p(C) p(G) p(T)
+.TP
+0.998150
+.IP
+0.000065 0.001755 0.000030
+.TP
+0.001449
+.IP
+0.000039 0.998460 0.000052
+.TP
+0.125811
+.IP
+0.000393 0.873431 0.000365
+.IP
+\-
+.IP
+\-
+.IP
+\-
+.IP
+0.004878 0.018097 0.118851 0.858174
+.IP
+0.000030 0.001637 0.000064 0.998269
+.IP
+\&...
+.PP
+The output files produced by prequel can get quite large.
+They
+can be encoded in a compact binary form using pbsEncode, e.g.,
+.IP
+pbsEncode anc.human\-mouse.probs codefile > anc.human\-mouse.bin
+.PP
+although this encoding results in some loss of precision.
+Encoded files can be decoded using pbsDecode, e.g.,
+.IP
+pbsDecode anc.human\-mouse.bin codefile > anc.human\-mouse.probs
+.PP
+For maximum efficiency, encode ancestral reconstructions on the
+fly using the \fB\-\-encode\fR option to prequel, e.g.,
+.IP
+prequel \fB\-\-encode\fR codefile mammals.fa mytree.mod anc
+.PP
+Prequel can also be useful in optimizing a code based on training
+data. The \fB\-\-suff\-stats\fR option produces a more compact output
+file, which can then be fed to pbsTrain, e.g.,
+.IP
+prequel \fB\-\-suff\-stats\fR mammals.fa mytree.mod training
+pbsTrain training.stats > mammals.code
+.SH OPTIONS
+.HP
+\fB\-\-seqs\fR, \fB\-s\fR <seqlist>
+.TP
+Only produce output for specified sequences.
+Argument should
+be comma\-separated list of names of ancestral nodes.
+.HP
+\fB\-\-exclude\fR, \fB\-x\fR
+(for use with \fB\-\-seqs\fR) Exclude rather than include specified
+sequences.
+.HP
+\fB\-\-keep\-gaps\fR, \fB\-k\fR
+.TP
+Retain gaps in output, as described above.
+.HP
+\fB\-\-no\-probs\fR, \fB\-n\fR
+.TP
+Instead of reporting a probability distribution for each ancestral
+base, output the base with the maximum posterior probability.
+Output will be in FASTA format to files having suffix ".fa" rather
+than ".probs". If used with \fB\-\-keep\-gaps\fR, gap characters ('\-') will
+appear in reconstructed sequences.
+.HP
+\fB\-\-suff\-stats\fR, \fB\-S\fR
+.IP
+Output a table of probability vectors and counts, pooling
+together all nodes of the tree (or a subset defined by
+\fB\-\-seqs\fR). Produces a file that can be used for code estimation
+by pbsTrain. Output file will have suffix ".stats".
+.HP
+\fB\-\-encode\fR, \fB\-e\fR <code_file>
+Encode probabilities using given code and output as binary
+files. Output files will have suffix ".bin" rather than ".probs"
+.HP
+\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
+.IP
+Alignment format (default is to guess format from file content).
+Note that the program msa_view can be used for conversion.
+.HP
+\fB\-\-refseq\fR, \fB\-r\fR <fname>
+.IP
+(for use with \fB\-\-msa\-format\fR MAF) Read the complete text of the
+reference sequence from <fname> (FASTA format) and combine it
+with the contents of the MAF file to produce a complete,
+ordered representation of the alignment. The reference
+sequence of the MAF file is assumed to be the one that appears
+first in each block.
+.HP
+\fB\-\-gibbs\fR, \fB\-G\fR <nsamples>
+.IP
+(experimental) Estimate posterior probabilities by Gibbs sampling
+rather than by the sum\-product algorithm. Sample each sequence
+<nsamples> times and estimate posterior probabilities as fraction
+of times each base appeared at each position. This option is used
+by default if a dinucleotide or trinucleotide model is given (exact
+inference not possible). NOT YET IMPLEMENTED
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Produce this help message.
diff --git a/debian/help2man/refeature.1 b/debian/help2man/refeature.1
new file mode 100644
index 0000000..1f42112
--- /dev/null
+++ b/debian/help2man/refeature.1
@@ -0,0 +1,96 @@
+.TH REFEATURE "1" "May 2016" "refeature 1.4" "User Commands"
+.SH NAME
+refeature \- Read a file representing a set of features, optionally
+.SH SYNOPSIS
+refeature [OPTIONS] <infile>
+.SH DESCRIPTION
+Read a file representing a set of features, optionally
+alter the set in one or more of several possible ways, then
+output it in the desired format. Input and output formats
+may be GFF, BED, or genepred.
+.PP
+The input format is recognized automatically, but autorecognition requires a 'seekable' input stream (e.g., an
+actual file rather than a pipe from stdin).
+.SH OPTIONS
+.HP
+\fB\-\-include\-only\fR, \fB\-i\fR <types>
+Include only features of the specified types (comma\-delimited list);
+filter out everything else.
+.HP
+\fB\-\-include\-groups\fR, \fB\-l\fR <file>
+.IP
+Include only groups whose names are listed in the specified file.
+Group names in file must be delimited by white\-space (can be on
+any number of lines).
+.HP
+\fB\-\-sort\fR, \fB\-s\fR
+.IP
+Sort features primarily by start position and secondarily
+by end position (usually has desired effect in case of short
+overlapping features, e.g., start & stop codons). Features
+will be sorted both across groups and within groups, but members
+of a group will be kept together.
+.HP
+\fB\-\-unique\fR, \fB\-u\fR
+.IP
+Ensures that output contains no overlapping groups (or
+subgroups, if \fB\-e\fR). If groups overlap, the one with the highest
+score (if available) or longest length (if no score) is kept and
+others are discarded. Warning: long UTRs can have undesirable
+results; filter out UTR exons to avoid.
+.HP
+\fB\-\-groupby\fR, \fB\-g\fR <tag>
+Group features according to specified tag (default "transcript_id")
+.HP
+\fB\-\-exongroup\fR, \fB\-e\fR <tag>
+.IP
+Sub\-group features into contiguous sets, and define
+sub\-groups using specified tag (e.g., "exon_id"). Can be
+used to group the features describing individual exons, e.g.,
+each CDS and its flanking splice sites. Only features in the
+same major group will be included in the same minor group
+(e.g., exons of the same transcript).
+.HP
+\fB\-\-fix\-start\-stop\fR, \fB\-f\fR
+.IP
+Ensure that CDS features include start codons and exclude stop
+codons, as required by the GTF2 standard. Assumes at most one
+start_codon and at most one stop_codon per group.
+.HP
+\fB\-\-add\-utrs\fR, \fB\-U\fR
+.IP
+Create UTR features for portions of exons outside CDS (only
+useful with GFF output; features must be grouped at level
+of transcript).
+.HP
+\fB\-\-add\-introns\fR, \fB\-I\fR
+.IP
+Create intron features between exons (only useful with GFF output;
+features must be grouped at level of transcript).
+.HP
+\fB\-\-add\-signals\fR, \fB\-S\fR
+Adds features for start and stop codons and 3' and 5' splice
+sites (only useful with GFF output; features must be grouped
+at level of transcript). Start and stop codons will be added
+as required by the GTF2 standard (\fB\-\-fix\-start\-stop\fR is not
+necessary). Warning: does not correctly handle case of splice
+site in middle of start or stop codon.
+.HP
+\fB\-\-output\fR, \fB\-o\fR gff|bed|genepred|wig
+Output format (default gff).
+Note that wig output is fixedStep
+can only be used if all elements have a score and are of equal
+length.
+.HP
+\fB\-\-simplebed\fR, \fB\-b\fR
+.IP
+(for use with \fB\-\-output\fR bed) Create a separate line for each
+feature in bed output (by default, all features of a group are
+described by a single line).
+.HP
+\fB\-\-discards\fR, \fB\-d\fR <fname>
+.IP
+Write any discarded features to specified file.
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+Print this help message.
diff --git a/debian/help2man/stringiphy.1 b/debian/help2man/stringiphy.1
new file mode 100644
index 0000000..080bcb9
--- /dev/null
+++ b/debian/help2man/stringiphy.1
@@ -0,0 +1,17 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH STRINGIPHY "1" "May 2016" "stringiphy 1.4" "User Commands"
+.SH NAME
+stringiphy \- Attempt to string together predicted exons into full transcripts
+.SH DESCRIPTION
+Attempt to string together predicted exons into full transcripts
+or gene fragments.
+.SH USAGE
+stringiphy [OPTIONS] <exons.gff>
+.IP
+(Predictions should be sorted and non\-overlapping; use
+\&'refeature \fB\-\-sort\fR \fB\-\-unique\fR')
+.SH OPTIONS
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
diff --git a/debian/help2man/treeGen.1 b/debian/help2man/treeGen.1
new file mode 100644
index 0000000..a5b46f9
--- /dev/null
+++ b/debian/help2man/treeGen.1
@@ -0,0 +1,34 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH TREEGEN "1" "May 2016" "treeGen 1.4" "User Commands"
+.SH NAME
+treeGen \- Enumerate rooted tree topologies, subject to constraints on
+.SH DESCRIPTION
+Enumerate rooted tree topologies, subject to constraints on
+monophyletic groups. An outgroup is assumed to be specified.
+.SH SYNOPSIS
+treeGen spec1,spec2,spec3,... [group1,group2,...] > outfile
+OR
+.IP
+treeGen '*speciesFile' ['*groupFile'] > outfile
+.IP
+(where speciesFile/groupFile contain whitespace\-delimited names)
+The last species listed is assumed to be the outgroup.
+.IP
+The optional "groups" classification can be used to define
+monophyletic groups. Each species may be assigned a nonnegative
+integer indicating its group, with 0 indicating no group
+assignment. The integers should appear in the same order as the
+species names. For example,
+.IP
+treeGen human,chimp,macaque,mouse,rat,dog,horse,fugu 1,1,1,2,2,0,0,0
+.IP
+could be used to generate all topologies of the specified vertebrate
+species such that the primates (human, chimp, and macaque) and the
+rodents (mouse and rat) appear as monophyletic groups. The outgroup
+should always be assigned a group of 0 (a nonzero value will be
+ignored).
+.SH OPTIONS
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+.IP
+Print this help message.
diff --git a/debian/help2man/tree_doctor.1 b/debian/help2man/tree_doctor.1
new file mode 100644
index 0000000..b539ca8
--- /dev/null
+++ b/debian/help2man/tree_doctor.1
@@ -0,0 +1,151 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH TREE_DOCTOR "1" "May 2016" "tree_doctor 1.4" "User Commands"
+.SH NAME
+tree_doctor \- Scale, prune, merge, and otherwise tweak phylogenetic trees.
+.SH DESCRIPTION
+Scale, prune, merge, and otherwise tweak phylogenetic trees.
+Expects input to be a tree model (.mod) file unless
+filename ends with '.nh' or \fB\-n\fR option is used, in which case
+it will be expected to be a tree file in Newick format.
+.SH USAGE
+tree_doctor [OPTIONS] <file.mod>|<file.nh>
+.SH OPTIONS
+.HP
+\fB\-\-prune\fR, \fB\-p\fR <list>
+Remove all leaves whose names are included in the given list
+(comma\-separated), then remove nodes and combine branches
+to restore as a complete binary tree (i.e., with each
+node having zero children or two children). This option is
+applied *before* all other options.
+.HP
+\fB\-\-prune\-all\-but\fR, \fB\-P\fR <list>
+.IP
+Like \fB\-\-prune\fR, but remove all leaves *except* the ones specified.
+.HP
+\fB\-\-get\-subtree\fR, \fB\-g\fR <node_name>
+Like \fB\-\-prune\fR, but remove all leaves who are not descendants of
+node. (Note: implies \fB\-\-name\-ancestors\fR if given node not
+explicitly named in input tree)
+.HP
+\fB\-\-rename\fR, \fB\-r\fR <mapping>
+Rename leaves according to the given mapping.
+The format of
+<mapping> must be: "oldname1 \-> newname1 ; oldname2 \->
+newname2 ; ...". This option is applied *after* all other
+options (i.e., old names will be used for \fB\-\-prune\fR, \fB\-\-merge\fR,
+etc.)
+.HP
+\fB\-\-scale\fR, \fB\-s\fR <factor>
+.IP
+Scale all branches by the specified factor.
+.HP
+\fB\-\-name\-ancestors\fR, \fB\-a\fR
+.TP
+Ensure names are assigned to all ancestral nodes.
+If a node
+.IP
+is unnamed, create a name by concatenating the names of a leaf
+from its left subtree and a leaf from its right subtree.
+.HP
+\fB\-\-label\-subtree\fR, \fB\-L\fR <node[+]:label>
+Add a label to the subtree of the named node.
+If the node name
+.IP
+is followed by a "+" sign, then the branch leading to that node
+is included in the subtree. This may be used multiple times to add
+more than one label, though a single branch may have only one
+label. \fB\-\-label\-subtree\fR and \fB\-\-label\-branches\fR options are parsed in
+the order given, so that later uses may override earlier ones.
+Labels are applied *after* all pruning, re\-rooting, and re\-naming
+options are applied.
+.HP
+\fB\-\-label\-branches\fR, \fB\-l\fR <branch1,branch2,...:label>
+.TP
+Add a label to the branches listed.
+Branches are named by the name
+.TP
+of the node which descends from that branch.
+See \fB\-\-label\-subtree\fR
+.IP
+above for more information.
+.HP
+\fB\-\-tree\-only\fR, \fB\-t\fR
+Output tree only in Newick format rather than complete tree model.
+.HP
+\fB\-\-no\-branchlen\fR, \fB\-N\fR
+(Implies \fB\-\-tree\-only\fR).
+Output only topology in Newick format.
+.HP
+\fB\-\-dissect\fR, \fB\-d\fR
+In place of ordinary output, print a description of the id,
+name, parent, children, and distance to parent for each node
+of the tree. Sometimes useful for debugging. Can be used with
+other options.
+.HP
+\fB\-\-branchlen\fR, \fB\-b\fR
+.IP
+In place of ordinary output, print the total branch length of
+the tree that would have been printed.
+.HP
+\fB\-\-depth\fR, \fB\-D\fR <node_name>
+In place of ordinary output, report distance from named node to
+root
+.HP
+\fB\-\-reroot\fR, \fB\-R\fR <node_name>
+.IP
+Reroot tree at internal node with specified name.
+.HP
+\fB\-\-subtree\fR, \fB\-S\fR <node_name>
+(for use with \fB\-\-scale\fR)
+Alter only the branches in the subtree
+beneath the specified node.
+.HP
+\fB\-\-with\-branch\fR, \fB\-B\fR <node_name>
+.IP
+(For use with \fB\-\-reroot\fR or \fB\-\-subtree\fR) include branch above specified
+node with subtree beneath it.
+.HP
+\fB\-\-merge\fR, \fB\-m\fR <file2.mod> | <file2.nh>
+Merge with another tree model or tree.
+The primary model
+(<file.mod>) must have a subset of the species (leaves) in the
+secondary model (<file2.mod>), and the primary tree must be a
+proper subtree of the secondary tree (i.e., the subtree of the
+secondary tree beneath the LCA of the species in the primary
+tree must equal the primary tree in terms of topology and
+species names). If a full tree model is given for the
+secondary tree, only the tree will be considered. The merged
+tree model will have the rate matrix, equilibrium frequencies,
+and rate distribution of the primary model, but a merged tree
+that includes all species from both models. The trees will be
+merged by first scaling the secondary tree such that the
+subtree corresponding to the primary tree has equal overall
+length to the primary tree, then combining the primary tree
+with the non\-overlapping portion of the secondary tree. The
+names of matching species (leaves) must be exactly equal.
+.HP
+\fB\-\-extrapolate\fR, \fB\-e\fR <phylog.nh> | default
+Extrapolate to a larger set of species based on the given
+phylogeny (Newick\-format). The primary tree must be a subtree
+of the phylogeny given in <phylog.nh>, but it need not be
+a "proper" subtree (see \fB\-\-merge\fR). A copy will be created
+of the larger phylogeny then scaled such that the total branch
+length of the subtree corresponding to the primary tree equals
+the total branch length of the primary tree; this new version
+will then be used in place of the primary tree. If the string
+"default" is given instead of a filename, then a phylogeny
+for 25 vertebrate species, estimated from sequence data for
+Target 1 (CFTR) of the NISC Comparative Sequencing Program
+(Thomas et al., Nature 424:788\-793, 2003), will be assumed.
+This option is similar to merge but differs in that the branch
+length proportions of the output tree come completely from the
+larger tree and the smaller tree doesn't have to be a proper
+subset of the larger tree.
+.HP
+\fB\-\-newick\fR,\-n
+.IP
+The input file is in Newick format (necessary if file name does
+not end in .nh)
+.HP
+\fB\-\-help\fR, \fB\-h\fR
+Print this help message.
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..ce81b16
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/help2man/*.1
diff --git a/debian/rules b/debian/rules
index 1023c59..91f4c5d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,19 +2,6 @@
# DH_VERBOSE := 1
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
-#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
-#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
-#GIT_TAG := $(subst ~,_,$(VERSION))
-
-# alternatively to manually set those variables, you can
-# include /usr/share/dpkg/default.mk
-# and use what is set there.
-
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
--
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