Commit 883c8140 authored by Andreas Tille's avatar Andreas Tille
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New upstream version 3.0.3+dfsg

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doc/README.html

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doc/README.itex.xml

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@@ -160,7 +160,15 @@ However, note that this might conflict with R installed from other places, such 
    </section>



    <section><info><title>Install on Linux</title></info>

    <section><info><title>Install BAli-Phy using executables from website</title></info>



    <section><info><title>Install BAli-Phy using <command>apt-get</command> (recommended if using <emphasis>Debian: unstable</emphasis>)</title></info>

    <screen><prompt>%</prompt> <userinput>sudo apt-get install bali-phy</userinput></screen>

    Check that the executable runs:

    <screen><prompt>%</prompt> <userinput>bali-phy --version</userinput></screen>

    If you install with <command>apt-get</command>, you don't need to do anything extra to put bali-phy in your PATH.

    </section>



    <section><info><title>Install BAli-Phy using executables from website (alternative)</title></info>



    <para>First install <command>wget</command>.  If you have Debian or Ubuntu Linux, type:

    <screen><prompt>%</prompt> <userinput>sudo apt-get install wget</userinput></screen>
@@ -196,7 +204,7 @@ However, note that this might conflict with R installed from other places, such 
    <section><title>Is bali-phy in your PATH already?</title>

<para> First check if the executable is in your PATH.

<screen><prompt>%</prompt> <userinput>bali-phy --version</userinput></screen>

If this shows version info, then <command>bali-phy</command> is already in your PATH and you can skip this section.  This should be true if you installed <command>bali-phy</command> using homebrew, or if you've already added it to your PATH.</para>

If this shows version info, then <command>bali-phy</command> is already in your PATH and you can skip this section.  This should be true if you installed <command>bali-phy</command> using a package manager such as homebrew or apt, or if you've already added it to your PATH.</para>

<para>If bali-phy is not in your path, then you should see:

<screen><prompt>%</prompt> <userinput>bali-phy --version</userinput>

bali-phy: command not found.</screen>

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doc/man/alignment-thin.md

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# SYNOPSIS



**alignment-thin** _alignment-file_

**alignment-thin** _alignment-file_ [OPTIONS]



# DESCRIPTION



Remove sequences or columns from an alignment.



# ALLOWED OPTIONS:

# GENERAL OPTIONS:

**-h**, **--help**

: produce help message

: Print usage information.



**--align** _arg_

: file with sequences and initial alignment

**-v**, **--verbose**

: Output more log messages on stderr.



**--find-dups** _arg_

: for each other sequence, find the closest sequence



# SEQUENCE FILTERING OPTIONS:

**--cutoff** _arg_

: only leave taxa with more mismatches than this value

: Keep only sequence with more mismatches than _arg_.



**--longer-than** _arg_

: only leave taxa w/ sequences longer than this

: Keep only sequences longer than _arg_.



**--shorter-than** _arg_

: only leave taxa w/ sequences shorter than this



**--down-to** _arg_

: number of taxa to keep

: Keep only sequence sequences shorter than _arg_.



**--keep** _arg_

: comma-separated list of taxon names to keep - remove others

: Keep only sequences in comma-separated list _arg_.



**--min-letters** _arg_

: Remove columns with fewer letters.

**--remove** _arg_

: Remove sequences in comma-separated list _arg_.



**-v**, **--verbose**

: Output more log messages on stderr.

**--down-to** _arg_

: Remove similar sequences down to _arg_ sequences.



**--show-lengths**

: just print out sequence lengths

**--remove-crazy** _arg_

: Remove _arg_ sequences that are missing too many conserved sites.



**--conserved** _arg_ (=0.75)

: Fraction of sequences that must contain a letter for it to be considered conserved.



**--sort**

: Sort partially ordered columns to minimize the number of visible indels.



# COLUMN FILTERING OPTIONS:

**--min-letters** _arg_

: Remove columns with fewer than _arg_ letters.



**--remove-unique** _arg_

: Remove insertions in a single sequence if longer than this many letters

: Remove insertions in a single sequence if longer than _arg_ letters



**--remove-crazy** _arg_

: Remove sequence that have deleted conserved sites



**--remove** _arg_

: comma-separated list of taxon names to remove

# OUTPUT OPTIONS:

**--sort**

: Sort partially ordered columns to group similar gaps.



**--conserved-fraction** _arg_ (=0.75)

: Fraction of sequences that must contain a letter for it to be considered conserved.

**--show-lengths**

: Just print out sequence lengths.



**--find-dups** _arg_

: For each sequence, find the closest other sequence.





# REPORTING BUGS: