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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 citations

 (16)
library_books

Clustering of Pan and Core genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

2018
BMC Genomics
PMCID: 5937832
PMID: 29690879
DOI: 10.1186/s12864-018-4601-5

[…] fy which gene or set of genes represents most closely the pan-genome-phylogenetic tree of L. delbrueckii, the tree of each core gene was compared to the tree of the pan genome of L. delbrueckii using TOPD/FMTS [] and CLC Workbench 8 (CLC Genomic, Aarhus, Denmark). Each homologous gene set from the core genome was imported as multi-entry FASTA into CLC Genomic Workbench 8. The genes were aligned us […]

library_books

Candidate genes for migration do not distinguish migratory and non migratory birds

2017
PMCID: 5522501
PMID: 28585043
DOI: 10.1007/s00359-017-1184-6

[…] within each branch. Random divergence (‘random tree’) was generated shuffling branches randomly from the gene trees obtained, in order to avoid bias regarding the method of random trees generation by TOPD/fmts that only randomises taxa, but not branches for the statistical comparison. Restricting these analyses to exclusively Passerine species allowed us to analyse the effects of the evolutionary […]

library_books

Dynamics of genome change among Legionella species

2016
Sci Rep
PMCID: 5025774
PMID: 27633769
DOI: 10.1038/srep33442

[…] All genes families with at least three members in each of Clades 1 to 3 were clustered using UPGMA. Each resulting tree was tested using the imonophyletic command of the R ape package and also using TOPD/FMTS (Version 3.3), where the former was implemented to determine if genes from the same clade formed monophyletic groups and the latter to check whether the topology of each of the accessory gen […]

library_books

Marker genes that are less conserved in their sequences are useful for predicting genome wide similarity levels between closely related prokaryotic strains

2016
Microbiome
PMCID: 4853863
PMID: 27138046
DOI: 10.1186/s40168-016-0162-5

[…] nce matrix values were one minus the AAIs or one minus the percent identities of a specific marker gene. Split distance (equivalent to the Robinson-Foulds distance) between trees was calculated using TOPD/FMTS software []. […]

call_split

Geological Changes of the Americas and their Influence on the Diversification of the Neotropical Kissing Bugs (Hemiptera: Reduviidae: Triatominae)

2016
PLoS Negl Trop Dis
PMCID: 4825970
PMID: 27058599
DOI: 10.1371/journal.pntd.0004527
call_split See protocol

[…] Four topologies were obtained and, to evaluate the discrepancies among them, the phylogenies were compared pairwise using TOPD/FMTS []. The algorithm used, namely, Disagree, shows not only the number of discordant nodes but also the taxa that are discordant. The comparison between the different topologies, obtained throu […]

call_split

Global Patterns of Protein Domain Gain and Loss in Superkingdoms

2014
PLoS Comput Biol
PMCID: 3907288
PMID: 24499935
DOI: 10.1371/journal.pcbi.1003452
call_split See protocol

[…] To determine congruence between abundance and occurrence trees, we used the nodal module implemented in the TOPD/FMTS package ver. 3.3 . 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 for i […]

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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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