[med-svn] r79 - trunk/packages/amap-align/trunk/debian

[Charles Plessy]

Author: charles-guest
Date: 2006-07-09 07:41:01 +0000 (Sun, 09 Jul 2006)
New Revision: 79

Removed:
   trunk/packages/amap-align/trunk/debian/amap-align.1
Modified:
   trunk/packages/amap-align/trunk/debian/rules
Log:
Clean the manpage

Deleted: trunk/packages/amap-align/trunk/debian/amap-align.1
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap-align.1	2006-07-09 07:35:24 UTC (rev 78)
+++ trunk/packages/amap-align/trunk/debian/amap-align.1	2006-07-09 07:41:01 UTC (rev 79)
@@ -1,152 +0,0 @@
-.\"Generated by db2man.xsl. Don't modify this, modify the source.
-.de Sh \" Subsection
-.br
-.if t .Sp
-.ne 5
-.PP
-\fB\\$1\fR
-.PP
-..
-.de Sp \" Vertical space (when we can't use .PP)
-.if t .sp .5v
-.if n .sp
-..
-.de Ip \" List item
-.br
-.ie \\n(.$>=3 .ne \\$3
-.el .ne 3
-.IP "\\$1" \\$2
-..
-.TH "AMAP" 1 "mai 3, 2006" "" ""
-.SH NAME
-amap-align \- Protein multiple alignment by sequence annealing
-.SH "SYNOPSIS"
-.ad l
-.hy 0
-.HP 11
-\fBamap\-align\fR [\fB\fIOPTION\fR\fR] [\fIMFAFILE\fR] [\fIMFAFILE\fR]
-.ad
-.hy
-
-.SH "DESCRIPTION"
-
-.PP
-On Debian™ systems, the \fBamap\fR command has been renamed \fBamap\-align\fR because there was already anonther tool called \fBamap\fR (which performs some computer network diagnostics)
-
-.PP
-AMAP is a tool to perform multiple alignment of peptidic sequences\&. It utilizes posterior decoding, and a sequence\-annealing alignment, instead of the traditional progressive alignment method\&. It is the only alignment program that allows to control the sensitivity / specificity tradeoff\&. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation\&.
-
-.PP
-In its default configuration, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score \- a new alignment accuracy measure, based on a metric for the multiple\-alignment space, which integrates sensitivity and specificity into a single balanced measure\&. AMA is defined as the fraction of correctly aligned residues (either to another residue or to a gap) out of the total number of residues in all the sequences\&.
-
-.PP
-\fBamap\-align\fR aligns sequences provided in MFA format\&. This format consists of multiple sequences\&. Each sequence in MFA format begins with a single\-line description, followed by lines of sequence data\&. The description line is distinguished from the sequence data by a greater\-than (``>'') symbol in the first column\&.
-
-.SH "OPTIONS"
-
-.TP
-\fB\-clustalw\fR
-use CLUSTALW output format instead of MFA
-
-.TP
-\fB\-c\fR \fB\-\-consistency\fR \fIREPS\fR
-use 0 <= \fIREPS\fR <= 5 (default: 0) passes of consistency transformation
-
-.TP
-\fB\-ir\fR \fB\-\-iterative\-refinement\fR \fIREPS\fR
-use 0 <= \fIREPS\fR <=1000 (default: 0) passes of iterative\-refinement
-
-.TP
-\fB\-pre\fR \fB\-\-pre\-training\fR \fIREPS\fR
-use 0 <= \fIREPS\fR <= 20 (default: 0) rounds of pretraining
-
-.TP
-\fB\-pairs\fR
-generate all\-pairs pairwise alignments
-
-.TP
-\fB\-viterbi\fR
-use Viterbi algorithm to generate all pairs (automatically enables \fB\-pairs\fR)
-
-.TP
-\fB\-v\fR \fB\-\-verbose\fR
-Report progress while aligning (default: off)
-
-.TP
-\fB\-annot\fR \fIFILENAME\fR
-write annotation for multiple alignment to \fIFILENAME\fR
-
-.TP
-\fB\-t\fR \fB\-\-train\fR \fIFILENAME\fR
-compute EM transition probabilities, store in \fIFILENAME\fR (default: no training)
-
-.TP
-\fB\-e\fR \fB\-\-emissions\fR
-also reestimate emission probabilities (default: off)
-
-.TP
-\fB\-p\fR \fB\-\-paramfile\fR \fIFILENAME\fR
-read parameters from \fIFILENAME\fR (default: )
-
-.TP
-\fB\-a\fR \fB\-\-alignment\-order\fR
-print sequences in alignment order rather than input order (default: off)
-
-.TP
-\fB\-g\fR \fB\-\-gap\-factor\fR \fIGF\fR
-use \fIGF\fR as the gap\-factor parameter, set to 0 for best sensitivity, higher values for better specificity (default: 0\&.5)
-
-.TP
-\fB\-w\fR \fB\-\-edge\-weight\-threshold\fR \fIW\fR
-stop the sequence annealing process when best edge has lower weight than \fIW\fR, set to 0 for best sensitivity, higher values for better specificity (default: 0)
-
-.TP
-\fB\-prog\fR \fB\-\-progressive\fR
-use progresive alignment instead of sequence annealing alignment (default: off)
-
-.TP
-\fB\-noreorder\fR \fB\-\-no\-edge\-reordering\fR
-disable reordring of edges during sequence annealing alignment (default: off)
-
-.TP
-\fB\-maxstep\fR \fB\-\-use\-max\-stepsize\fR
-use maximum improvement step size instead of tGf edge ranking (default: off)
-
-.TP
-\fB\-print\fR \fB\-\-print\-posteriors\fR
-only print the posterior probability matrices (default: off)
-
-.SH "SEE ALSO"
-
-.PP
-The current version of AMAP uses the PROBCONS 1\&.09 code base for some of the input/output procedures, and for the calculation of posterior probabilities (see PROBCONS\&.README in \fI/usr/share/doc/amap\-align/\fR)\&. Future releases might implement the algorithm using a new independent code base\&. On Debian&#8482; systems, PROBCONS is available in the probcons package\&.
-
-.SH "REFERENCES"
-
-.PP
-For more details on AMAP and AMA, see Schwartz, Ariel S\&., Myers, Eugene W\&., and Pachter, Lior\&. Alignment Metric Accuracy (Submitted for publication)\&. For more details on sequence\-annealing, see Schwartz, Ariel S\&. and Pachter, Lior\&. Multiple Alignment by Sequence Annealing (Submitted for publication)\&.
-
-.PP
-PROBCONS was published in Do, C\&.B\&., Mahabhashyam, M\&.S\&.P\&., Brudno, M\&., and Batzoglou, S\&. 2005\&. PROBCONS: Probabilistic Consistency\-based Multiple Sequence Alignment\&. Genome Research 15: 330\-340\&.
-
-.SH "AUTHORS"
-
-.TP 3
-\(bu
-PROBCONS was written by Chuong Do\&.
-.TP
-\(bu
-AMAP algorithm implemented by Ariel Schwartz (<sariel at cs\&.berkeley\&.edu>)\&.
-.TP
-\(bu
-This manual page was written by Charles Plessy <charles\-debian\-nospam at plessy\&.org> for the Debian&#8482; system (but may be used by others)\&.
-.LP
-
-.SH "LICENCE"
-
-.PP
-AMAP comes with ABSOLUTELY NO WARRANTY\&. This is free software, and you are welcome to redistribute it under certain conditions\&. See the files README and README\&.PROBCONS for details\&.
-
-.PP
-This manpage is hereby placed in the public domain\&.
-

Modified: trunk/packages/amap-align/trunk/debian/rules
===================================================================
--- trunk/packages/amap-align/trunk/debian/rules	2006-07-09 07:35:24 UTC (rev 78)
+++ trunk/packages/amap-align/trunk/debian/rules	2006-07-09 07:41:01 UTC (rev 79)
@@ -38,7 +38,7 @@
 	dh_testroot
 	rm -f build-stamp
 	-$(MAKE) clean
-	dh_clean debian/probcons.1
+	dh_clean debian/amap-align.1
 
 install: build
 	dh_testdir