FamFetch protocols

View FamFetch computational protocol

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FamFetch specifications

Information


Unique identifier OMICS_13165
Name FamFetch
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
Java
Maintained Yes

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Maintainer


  • person_outline Guy Perriere <>

Publication for FamFetch

FamFetch in pipeline

2008
PMCID: 2600815
PMID: 19096706
DOI: 10.1371/journal.pgen.1000311

[…] (with default parameters), and phylogenetic trees with phyml . phylogenies are computed on conserved blocks of the alignments selected with gblocks . using the treepattern functionality of the famfetch client for homolens, which allows scanning for gene tree topologies , we selected sets of genes with or without duplications on specific branches of the vertebrate phylogenetic tree., […]


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FamFetch in publications

 (5)
PMCID: 3124429
PMID: 21663612
DOI: 10.1186/1471-2148-11-159

[…] leu is present in position 95. to understand the possible positive effects of the replacement of leu95 with trp we investigated the structural impact of this mutation on human β2-m., we used the famfetch tool with the entry name b2mg_human to search the hovergen database. the retrieved family, hbg006197, consisted of 130 protein sequences from 96 different species with gnathostomata […]

PMCID: 2949868
PMID: 20836842
DOI: 10.1186/1471-2148-10-276

[…] revealed (additional file )., our method can potentially be applied to obtain new epic loci for any phylogenetic group. three strategies can be followed. (i) using the last version of homolens, the famfetch tool, and the graphical tool developed in this study, one can isolate numerous new epic loci, eventually decreasing the stringency level allowing duplication nodes in some genomes, […]

PMCID: 2955734
PMID: 20551039
DOI: 10.1093/molbev/msq149

[…] 49 (march 2008; ) march 2008 being the date of release 49. genes are organized in families, which include precalculated alignments and phylogenies. the main advantage of the homolens system is the famfetch query system and the treepattern function (). we can scan for specific topologies among the 23,155 family trees. we selected four different branches of the evolution of animals (): 1) […]

PMCID: 2600815
PMID: 19096706
DOI: 10.1371/journal.pgen.1000311

[…] (with default parameters), and phylogenetic trees with phyml . phylogenies are computed on conserved blocks of the alignments selected with gblocks . using the treepattern functionality of the famfetch client for homolens, which allows scanning for gene tree topologies , we selected sets of genes with or without duplications on specific branches of the vertebrate phylogenetic tree., […]

PMCID: 2584045
PMID: 18834516
DOI: 10.1186/1471-2148-8-272

[…] is not fulfilled., in order to get a whole genome view of aquificales phylogenetic relationships, we queried the hogenom database (release 03, october 2005) using the treepattern program in famfetch []. hogenom is a database that clusters sequences from whole genomes into homologous gene families, and builds trees based on these families with phyml using a gamma law with 4 classes […]


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FamFetch institution(s)
INRIA Rhône-Alpes, Saint Ismier, France; Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard Lyon 1, Villeurbanne, France
FamFetch funding source(s)
This work has been supported by EEC, CNRS and INRIA.

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