TOPD/FMTS pipeline

TOPD/FMTS specifications

Information


Unique identifier OMICS_13096
Name TOPD/FMTS
Alternative name TOPological Distance/From Multiple To Single
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input format TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Medium
Version 3.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Pere Puigbo <>

Publication for TOPological Distance/From Multiple To Single

TOPD/FMTS IN pipelines

 (2)
2014
PMCID: 3907288
PMID: 24499935
DOI: 10.1371/journal.pcbi.1003452

[…] the ‘chglist’ option in paup*. trees were visualized using dendroscope ver. 3.0.14b [49]., to determine congruence between abundance and occurrence trees, we used the nodal module implemented in the topd/fmts package ver. 3.3 [50]. the module takes as input a set of trees in newick format and calculates a root mean squared deviation (rmsd) value for each pairwise comparison. the rmsd value is 0 […]

2009
PMCID: 2660368
PMID: 19284603
DOI: 10.1186/1471-2164-10-104

[…] [45] and trees were computed with phyml [46] using the wag amino acid substitution model of evolution [47] and four categories of substitution rates. similarities between trees were computed using topd/fmts with the split distance (a low split distance value is synonymous of a high number of common branches between the two trees) [48]. mean linkage hierarchical clustering was applied […]

TOPD/FMTS institution(s)
Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Tarragona, Spain; Bioinformatics Laboratory, National University of Ireland, Maynooth, Ireland
TOPD/FMTS funding source(s)
This work has been financed by the project BIO2003-07672 from the Ministerio de Ciencia y Tecnología of the Spanish Government.

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