Online

Allows the complete Ensembl gene database to be queried using phylogenetic patterns. PhyloPat offers the possibility of querying with binary phylogenetic patterns or regular expressions, or through a phylogenetic tree of the 39 included species. Users can also input a list of Ensembl, EMBL, EntrezGene or HGNC IDs to check which phylogenetic lineage any gene belongs to.

User report

Sort by:

1 user review

1 user review

Tim Hulsen's avatar image

Tim Hulsen

Very useful tool!

PhyloPat forum

No open topic.

PhyloPat classification

PhyloPat specifications

Restrictions to use:
None

Publications

  • (Hulsen et al., 2009) PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood. Nucleic acids research.
    PMID: 18832367
  • (Hulsen et al., 2006) PhyloPat: phylogenetic pattern analysis of eukaryotic genes. BMC bioinformatics.
    PMID: 16948844

PhyloPat support

Maintainer

Credits

Institution(s)

Computational Drug Discovery (CDD), CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen and Department of Molecular Design and Informatics, Schering-Plough, Molenstraat 110, 5340 BH Oss, The Netherlands

Funding source(s)

This work was part of BioRange SP3.2.2 project of the Netherlands Bioinformatics Centre (NBIC), and was supported financially by Schering-Plough corporation.

Link to literature

Related Phylogenetic inference tools

Most Recent Tools

POY
Desktop

POY

Supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene…

Supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc). POY is a phylogenetic analysis program that can perform true sequence…

FastME
Desktop
Web

FastME

Provides distance algorithms to infer phylogenies. FastME is based on balanced…

Provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing…

RSAT…
Web

RSAT matrix-clustering

Supports dynamic browsing of motif trees with custom collapse/expansion of…

Supports dynamic browsing of motif trees with custom collapse/expansion of branches. RSAT matrix-clustering also provides multiple ways to inspect the results: motif forest with branch motifs at each…

DPRml
Desktop

DPRml Distributed Phylogeny Reconstruction by maximum likelihood

Can harness the idle computing resources of any research institute to construct…

Can harness the idle computing resources of any research institute to construct large phylogenetic trees using maximum likelihood. DPRml uses an already proven maximum likelihood-based tree building…

16 related tools

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.