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<P><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB">I wish to introduce the TOPD/FMTS software to evaluate similarities and differences between phylogenetic trees. TOPD/FMTS can compare trees with leaf-sets that either completely or partially overlap and can be also used to compare two trees, one or both of which are multigene family trees.<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"><o:p>T</o:p></SPAN><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB">he version 1.0 of TOPD/FMTS implements the following methods to compare phylogenetic trees:<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"><o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"><SPAN style="mso-tab-count: 1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>- Split distance.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"><SPAN style="mso-tab-count: 1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>- Nodal distance.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"><SPAN style="mso-spacerun: yes">&nbsp;</SPAN><SPAN style="mso-tab-count: 1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>- Disagree.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"><SPAN style="mso-tab-count: 1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>- Taxa in common.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"><SPAN style="mso-tab-count: 1">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN>- Quartets.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-INDENT: 35.4pt; TEXT-ALIGN: justify"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB">- Triplets.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"><o:p>&nbsp;</o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt; TEXT-ALIGN: justify"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"><o:p></o:p></SPAN><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB">Each option is also complemented with a randomisation analysis to test the null hypothesis that the similarity between two trees is not better than chance expectation.<o:p></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"></SPAN>&nbsp;</P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB">TOPD/FMTS is freely available at: <A href="http://genomes.urv.cat/topd" target=1><FONT color=#3a2eb5>http://genomes.urv.cat/topd</FONT></A> .<o:p></o:p></SPAN></P><PRE><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB">For more details see the article <A href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm135v1?papetoc" target=1><FONT color=#800080>Puigbo et al. 2007. Bioinformatics doi: 10.1093/bioinformatics/btm135</FONT></A> .</SPAN></PRE><PRE><SPAN lang=EN-GB style="FONT-SIZE: 11pt; FONT-FAMILY: Arial; mso-fareast-font-family: SimSun; mso-ansi-language: EN-GB"></SPAN>&nbsp;</PRE><BR><BR>--------------------------------------------------------------------------------------------------------------------
<br>Pere Puigbň Avalos, PhD Student
<br>Evolutionary Genomics Group,
<br>Biochemistry and Biotechnology Department,
<br>Rovira i Virgily University.
<br>C/Marcelˇlí domingo s/n. 43007. Campus Sescelades. Tarragona.
<br>
<br>Phone: 0034.977.55.84.86
<br>Web Page: http://genomes.urv.cat
<br>E-mail: ppuigbo@urv.cat
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