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6,883,833,661 homologs retrieved from 7,652,822 Maximum Likelihood trees for 2,714 species from 12 public repositories

  1. Updated tree repositories
  2. Solved some minor issues
    1. strain-to-species mapping problems


2,286,510,661 homologs retrieved from 5,693,067 Maximum Likelihood trees for 2,435 species from 12 public repositories.

  1. Added new and updated previosly present repositories
    1. EggNOG update and added all divisions (previously only euNOG & KOG)
    2. Ensembl update (including Ensembl Genomes)
    3. Hogenom included
    4. OrthoMCL update
    5. PhylomeDB update
    6. TreeFAM update
    7. Fungal Orthogroups were deprecated due to small dabatase size and lack of updates
  2. Methodology changes:
    1. Species-oriented
    2. Gene-oriented
    3. Trees with multifucations included
    4. Evidence level now counting databases, to repositories ie. distinct phylomes
  3. Webserver changes
    1. New sequence information page
      1. ID information with links listed: internal, UniProt, external repositories
      2. Gene name and function
      3. GO function logo and GO functions
      4. Sequence in FASTA
    2. New tree information page
    3. Gene names accepted (with autocompletion)
    4. Species names accepted (with autocompletion)
    5. Functional tag clouds
    6. Rapid similarity search implemented
    7. RANDOM protein query for orthologs, sequence information and similarity search
  4. API changes
    1. HTTP requests introduced
    2. Improved Python API (available unpon request)
  5. Social media
    1. You are welcome to follow us on Twitter (@orthologs)