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<HTML>
<HEAD>
<TITLE>
EMBOSS
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<table align=center border=0 cellspacing=0 cellpadding=0>
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<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
PHYLOGENY MOLECULAR SEQUENCE
</font></b>
</td></tr>
</table>
<br>
<p>
<!--END OF HEADER-->
Phylogenetic molecular sequence methods
<p>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="distmat.html">distmat</a></td>
<td>
Create a distance matrix from a multiple sequence alignment
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/ednacomp.html">ednacomp</a></td>
<td>
DNA compatibility algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/ednadist.html">ednadist</a></td>
<td>
Nucleic acid sequence distance matrix program
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/ednainvar.html">ednainvar</a></td>
<td>
Nucleic acid sequence invariants method
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/ednaml.html">ednaml</a></td>
<td>
Phylogenies from nucleic acid maximum likelihood
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/ednamlk.html">ednamlk</a></td>
<td>
Phylogenies from nucleic acid maximum likelihood with clock
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/ednapars.html">ednapars</a></td>
<td>
DNA parsimony algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/ednapenny.html">ednapenny</a></td>
<td>
Penny algorithm for DNA
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/eprotdist.html">eprotdist</a></td>
<td>
Protein distance algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/eprotpars.html">eprotpars</a></td>
<td>
Protein parsimony algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/erestml.html">erestml</a></td>
<td>
Restriction site maximum likelihood method
</td>
</tr>
<tr>
<td><a href="../embassy/phylip/eseqboot.html">eseqboot</a></td>
<td>
Bootstrapped sequences algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fdiscboot.html">fdiscboot</a></td>
<td>
Bootstrapped discrete sites algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fdnacomp.html">fdnacomp</a></td>
<td>
DNA compatibility algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fdnadist.html">fdnadist</a></td>
<td>
Nucleic acid sequence distance matrix program
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fdnainvar.html">fdnainvar</a></td>
<td>
Nucleic acid sequence invariants method
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fdnaml.html">fdnaml</a></td>
<td>
Estimate nucleotide phylogeny by maximum likelihood
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fdnamlk.html">fdnamlk</a></td>
<td>
Estimates nucleotide phylogeny by maximum likelihood
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fdnamove.html">fdnamove</a></td>
<td>
Interactive DNA parsimony
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fdnapars.html">fdnapars</a></td>
<td>
DNA parsimony algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fdnapenny.html">fdnapenny</a></td>
<td>
Penny algorithm for DNA
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fdolmove.html">fdolmove</a></td>
<td>
Interactive Dollo or polymorphism parsimony
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/ffreqboot.html">ffreqboot</a></td>
<td>
Bootstrapped genetic frequencies algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fproml.html">fproml</a></td>
<td>
Protein phylogeny by maximum likelihood
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fpromlk.html">fpromlk</a></td>
<td>
Protein phylogeny by maximum likelihood
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fprotdist.html">fprotdist</a></td>
<td>
Protein distance algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fprotpars.html">fprotpars</a></td>
<td>
Protein parsimony algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/frestboot.html">frestboot</a></td>
<td>
Bootstrapped restriction sites algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/frestdist.html">frestdist</a></td>
<td>
Calculate distance matrix from restriction sites or fragments
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/frestml.html">frestml</a></td>
<td>
Restriction site maximum likelihood method
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fseqboot.html">fseqboot</a></td>
<td>
Bootstrapped sequences algorithm
</td>
</tr>
<tr>
<td><a href="../embassy/phylipnew/fseqbootall.html">fseqbootall</a></td>
<td>
Bootstrapped sequences algorithm
</td>
</tr>
</table>
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