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  • #1

    OrthoFinder: accurate gene families made easy!

    Hi All,

    I just wanted to post a shameless plug for our new gene family (orthogroup) finding software called OrthoFinder that has just come out in GenomeBiology.

    OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy - Genome Biology
    http://www.genomebiology.com/2015/16/1/157
    Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using real benchmark datasets we demonstrate that OrthoFinder is more accurate than other orthogroup inference methods by between 8 % and 33 %. Furthermore, we demonstrate the utility of OrthoFinder by providing a complete classification of transcription factor gene families in plants revealing 6.9 million previously unobserved relationships.


    If you looking to cluster protein coding genes from your newly sequenced genomes, or looking to do some comparative analysis of gene families in multiple species then please check it out and shout if you encounter any problems!
    Tags: None
  • #2
    New release of OrthoFinder

    Releases · davidemms/OrthoFinder
    https://github.com/davidemms/OrthoFinder/releases
    Phylogenetic orthology inference for comparative genomics - davidemms/OrthoFinder


    Faster, more options, added flexibility. Making gene families (orthogroups) from whole genomes with just one command just got even easier.

    Comment

    • #3
      How the SpeciesTreeAlignment

      Dear all

      Please , how the SpeciesTreeAlignment.fa is generated in orthofinder? this file is located inside the Alignement directory it contains the alignment for different orthogroups. I want to know if this was generated with the concatenation of the core orthgroups or with all the Orthogroups. Or any additional explanations. are welcome.

      Thanks in advance for your help

      DD

      Comment

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