[med-svn] r131 - trunk/packages/poa/trunk/debian
Charles Plessy
charles-guest at costa.debian.org
Tue Sep 26 06:48:13 UTC 2006
Author: charles-guest
Date: 2006-09-26 06:48:06 +0000 (Tue, 26 Sep 2006)
New Revision: 131
Modified:
trunk/packages/poa/trunk/debian/poa.1.xml
trunk/packages/poa/trunk/debian/rules
Log:
new manpage
Modified: trunk/packages/poa/trunk/debian/poa.1.xml
===================================================================
--- trunk/packages/poa/trunk/debian/poa.1.xml 2006-09-26 04:49:25 UTC (rev 130)
+++ trunk/packages/poa/trunk/debian/poa.1.xml 2006-09-26 06:48:06 UTC (rev 131)
@@ -5,7 +5,7 @@
<!ENTITY dhfirstname "<firstname>Charles</firstname>">
<!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhdate "<date>august 20, 2006</date>">
+ <!ENTITY dhdate "<date>september 26, 2006</date>">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
<!ENTITY dhusername "Charles Plessy">
@@ -41,79 +41,123 @@
<refnamediv>
<refname>&dhpackage;</refname>
- <refpurpose>performs multiple alignment of biological sequences.</refpurpose>
+ <refpurpose>align a set of sequences or alignments.</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
- <arg choice="opt">Options</arg>
+ <arg choice="opt">OPTIONS</arg>
<arg choice="opt">
- <replaceable>matrixfile</replaceable>
+ <replaceable>MATRIXFILE</replaceable>
</arg>
</cmdsynopsis>
+
+ <para>One of the <option>-read_fasta</option>, <option>-read_msa</option>, or <option>-read_msa_list</option> arguments must be used, since a sequence or alignment file is required.</para>
+
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para><command>POA</command> is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. Partial order alignment is an approach to MSA, which can be combined with existing methods such as progressive alignment. POA optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is 10 to 30 times faster than CLUSTALW.</para>
-
</refsect1>
+
<refsect1>
+ <title>EXAMPLE</title>
+ <para><command>poa</command> <option>-read_fasta</option> <filename>multidom.seq</filename> <option>-clustal</option> <filename>m.aln</filename> <filename>blosum80.mat</filename></para>
+ </refsect1>
+
+ <refsect1>
<title>OPTIONS</title>
<refsect2>
<title>INPUT</title>
<variablelist>
<varlistentry>
<term><option>-read_fasta</option>
- <parameter>FILENAME</parameter>
+ <parameter>FILE</parameter>
</term>
<listitem>
- <para>Reads in FASTA sequence file.</para>
+ <para>Read in FASTA sequence file.</para>
</listitem>
</varlistentry>
-
+
<varlistentry>
- <term><option>-tolower</option>
+ <term><option>-read_msa</option>
+ <parameter>FILE</parameter>
</term>
<listitem>
- <para>Forces FASTA sequences to lowercase (nucleotides in our matrix files).</para>
+ <para>Read in MSA alignment file.</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-toupper</option>
+ <term><option>-read_msa2</option>
+ <parameter>FILE</parameter>
</term>
<listitem>
- <para>Forces FASTA sequences to UPPERCASE (amino acids in our matrix files).</para>
+ <para>Read in second MSA file.</para>
</listitem>
</varlistentry>
- <varlistentry>
- <term><option>-read_po</option>
- <parameter>FILENAME</parameter>
+ <varlistentry>
+ <term><option>-subset</option>
+ <parameter>FILE</parameter>
</term>
<listitem>
- <para>Reads in PO file.</para>
+ <para>Filter MSA to include list of seqs in file.</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-subset</option>
- <parameter>FILENAME</parameter>
+ <term><option>-subset2</option>
+ <parameter>FILE</parameter>
</term>
<listitem>
- <para>Filters PO-MSA to include list of seqs in file.</para>
+ <para>Filter second MSA to include list of seqs in file.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-remove</option>
- <parameter>FILENAME</parameter>
+ <parameter>FILE</parameter>
</term>
<listitem>
- <para> Filters PO-MSA to exclude list of seqs in file.</para>
+ <para>Filter MSA to include list of seqs in file.</para>
</listitem>
</varlistentry>
+
+ <varlistentry>
+ <term><option>-remove2</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Filter second MSA to include list of seqs in file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-read_msa_list</option>
+ <parameter>FILE</parameter>
+ </term>
+ <listitem>
+ <para>Read an MSA from each filename listed in file.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-tolower</option>
+ </term>
+ <listitem>
+ <para>Force FASTA/MSA sequences to lowercase (nucleotides in our matrix files).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-toupper</option>
+ </term>
+ <listitem>
+ <para>Force FASTA/MSA sequences to UPPERCASE (amino acids in our matrix files).</para>
+ </listitem>
+ </varlistentry>
</variablelist>
</refsect2>
@@ -122,11 +166,25 @@
<variablelist>
<varlistentry>
- <term><option>-pair_score</option>
- <parameter>FILENAME</parameter>
+ <term><option>-do_global</option></term>
+ <listitem>
+ <para>Do global alignment.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-do_progressive</option></term>
+ <listitem>
+ <para>Perform progressive alignment using a guide tree built by neighbor joining from a set of sequence-sequence similarity scores.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-read_pairscores</option>
+ <parameter>FILE</parameter>
</term>
<listitem>
- <para>Reads tab-delimited file of sequence-sequence similarity scores for constructing a guide-tree and performing progressive alignment using PO-PO alignment steps.</para>
+ <para>Read tab-delimited file of similarity scores (If not provided, scores are constructed using pairwise sequence alignment.)</para>
</listitem>
</varlistentry>
@@ -134,7 +192,7 @@
<term><option>-fuse_all</option>
</term>
<listitem>
- <para>Fuses identical letters on align rings.</para>
+ <para>Fuse identical letters on align rings.</para>
</listitem>
</varlistentry>
</variablelist>
@@ -148,7 +206,7 @@
<term><option>-hb</option>
</term>
<listitem>
- <para>Performs heaviest bundling to generate consensi.</para>
+ <para>Perform heaviest bundling to generate consensi.</para>
</listitem>
</varlistentry>
@@ -157,7 +215,7 @@
<parameter>VALUE</parameter>
</term>
<listitem>
- <para> Bundles into heaviest bundle seqs with percent id >= <parameter>value</parameter>.</para>
+ <para>Include in heaviest bundle sequences with percent ID (as a fraction) >= <parameter>VALUE</parameter>.</para>
</listitem>
</varlistentry>
</variablelist>
@@ -167,63 +225,67 @@
<title>OUTPUT</title>
<variablelist>
- <varlistentry>
- <term><option>-best</option>
+ <varlistentry>
+ <term><option>-pir</option>
+ <parameter>FILE</parameter>
</term>
<listitem>
- <para>Restricts MSA output to heaviest bundles.</para>
+ <para>Write out MSA in PIR format.</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-pir</option>
- <parameter>FILENAME</parameter>
+ <term><option>-clustal</option>
+ <parameter>FILE</parameter>
</term>
<listitem>
- <para>Writes out MSA in PIR format.</para>
+ <para>Write out MSA in CLUSTAL format.</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-clustal</option>
- <parameter>FILENAME</parameter>
+ <term><option>-po</option>
+ <parameter>FILE</parameter>
</term>
<listitem>
- <para>Writes out MSA in CLUSTAL format.</para>
+ <para>Write out MSA in PO format.</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-po</option>
- <parameter>FILENAME</parameter>
- </term>
+ <term><option>-preserve_seqorder</option></term>
<listitem>
- <para>Writes out MSA in PO format.</para>
+ <para>Write out MSA with sequences in their input order.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-printmatrix</option>
- <parameter>LETTERSET</parameter>
+ <parameter>LETTERS</parameter>
</term>
<listitem>
- <para>Prints score matrix to stdout.</para>
+ <para>Print score matrix to stdout.</para>
</listitem>
</varlistentry>
<varlistentry>
+ <term><option>-best</option>
+ </term>
+ <listitem>
+ <para>Restrict MSA output to heaviest bundles (PIR only).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
<term><option>-v</option>
<option></option>
</term>
<listitem>
- <para>Runs in verbose mode.</para>
+ <para>Run in verbose mode (e.g. output gap penalties).</para>
</listitem>
</varlistentry>
</variablelist>
</refsect2>
-
- <para>Note: Either the <option>-read_fasta</option> or <option>-read_po</option> argument must be used with poa, since a FASTA file or PO file must be read in by poa.</para>
-
</refsect1>
<refsect1>
Modified: trunk/packages/poa/trunk/debian/rules
===================================================================
--- trunk/packages/poa/trunk/debian/rules 2006-09-26 04:49:25 UTC (rev 130)
+++ trunk/packages/poa/trunk/debian/rules 2006-09-26 06:48:06 UTC (rev 131)
@@ -50,7 +50,7 @@
dh_installdocs README
dh_installexamples multidom.seq
dh_install
- dh_installman poa.1
+ dh_installman debian/poa.1
dh_link
dh_strip
dh_compress
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