fas2phy

convert fasta (aligned sequences) to phylip format

Supports reading and writing sequences for different formats (currently interleaved and sequential formats for 'FASTA' and 'PHYLIP'), file conversion, and manipulation (e.g. filter sequences that contain specify pattern, export consensus sequence from an alignment).

Guangchuang Yu

seqmagick

Sequence Manipulation Utilities

fas2phy function

<dl><dt>fasfile</dt>
<dd>aligned sequences in fasta format</dd>
<dt>outfile</dt>
<dd>output file</dd>
<dt>type</dt>
<dd>one of interleaved and sequential</dd></dl>

Arguments

Guangchuang Yu
fa_file &lt;- system.file("extdata/HA.fas", package="seqmagick")
phy_file &lt;- tempfile(fileext = ".phy")
fas2phy(fa_file, phy_file)

Author

fas2phy — fas2phy

<dl>

<dt>fasfile</dt>
<dd>aligned sequences in fasta format</dd>


<dt>outfile</dt>
<dd>output file</dd>


<dt>type</dt>
<dd>one of interleaved and sequential</dd>

</dl>

fas2phy: fas2phy

Description

Usage

Value

Arguments

Author