GreenPhyl Information



20/02/2014

Release Notes of version 4

We are pleased to announce a new release of GreenPhylDB (version 4)

Database content


The following genomes were added:
  1. Amborella trichopoda v1
  2. Cajanus cajan v1
  3. Cicer arietinum v1
  4. Citrus sinensi s v1
  5. Elaeis guineensis v1
  6. Gossypium raimondii v1
  7. Hordeum vulgare v1
  8. Lotus japonicus v2.5
  9. Musa balbisiana v1
  10. Phaseolus vulgaris v1
  11. Picea abies v1
  12. Setaria italica v1
  13. Solanum lycopersicum v2.4
  14. Solanum tuberosum v3

We also updated the following versions:

  1. Oryza sativa ( v6 to v7)
  2. Ostreococcus tauri (v2 to v4)
  3. Vitis vinifera (8x to 12x)

Sources and versions are listed in the documentation section.

Phylogenetic analyses and homology predictions

As for the previous versions, phylogenetic analyses and Reciprocical Blast Hits were performed. 5545 gene trees out of the 8347 clusters at level 1 are available. This number is lower than for the previous version and this is due to two main reasons. First, with addtional genomes the size of gene families is increasing drastically and calculation are more and more computer intensive. Second, protein annotations are increasingly heterogeneous in term of annotations quality, leading to multiple alignments that did not pass our quality filters and therefore phylogeny have not been launched because the orthology predictions would not be reliable enough. We plan to adress this issue and will expand the number of gene families with gene tree analyses.For each computed gene tree, we now provide statitics on the alignment, filtration, and evolution of the gene tree.

Further statistics about the database are available in the statistics section

New tools and functionalities

Gene tree display

It is now possible to filter the species displayed in a gene tree but keeping into account the phylogeny performed for the whole set of species. This feature is particularly useful for big genes trees and/or if you are only interested in a subset of species.


treeFilter

TreePattern

A new way to explore phylogenetic trees. Define your evoltion pattern and look at the matching trees.

treepattern

Custom families

We developed a user-friendly interface allowing either to customize pre-computed protein sequence clusters or to create new ones based on prior knowledge of a given gene family. Information can be then shared with collaborators and/or reviewers with a unique URL. We will therefore an addtional gene family list section containing customised gene families by users who decide to share it publically. This tool intends also to support publication process.

Custom families

Gene ontology Browser

It now possible to browse the full Gene Ontology, which used to be restricted to PlantSlim terms.


Should you have any questions, please do not hesitate to contact us. Please note that the version 1, 2 and 3 remain accessible at the following address:
http://www.greenphyl.org

The GreenPhyl team