title: aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
abstract: We report a new web server, aLeaves (http://aleaves.cdb.riken.jp/), for homologue collection from diverse animal genomes. In molecular comparative studies involving multiple species, orthology identification is the basis on which most subsequent biological analyses rely. It can be achieved most accurately by explicit phylogenetic inference. More and more species are subjected to large-scale sequencing, but the resultant resources are scattered in independent project-based, and multi-species, but separate, web sites. This complicates data access and is becoming a serious barrier to the comprehensiveness of molecular phylogenetic analysis. aLeaves, launched to overcome this difficulty, collects sequences similar to an input query sequence from various data sources. The collected sequences can be passed on to the MAFFT sequence alignment server (http://mafft.cbrc.jp/alignment/server/), which has been significantly improved in interactivity. This update enables to switch between (i) sequence selection using the Archaeopteryx tree viewer, (ii) multiple sequence alignment and (iii) tree inference. This can be performed as a loop until one reaches a sensible data set, which minimizes redundancy for better visibility and handling in phylogenetic inference while covering relevant taxa. The work flow achieved by the seamless link between aLeaves and MAFFT provides a convenient online platform to address various questions in zoology and evolutionary biology.
authors.affiliation: Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan. shigehiro-kuraku@cdb.riken.jp
authors.forename: Shigehiro
authors.initials: S
authors.lastname: Kuraku
authors.forename: Christian M
authors.initials: CM
authors.lastname: Zmasek
authors.forename: Osamu
authors.initials: O
authors.lastname: Nishimura
authors.forename: Kazutaka
authors.initials: K
authors.lastname: Katoh
mesh_terms: D000818:Animals; D000076246:CCCTC-Binding Factor; D005796:Genes; D005801:Genes, Homeobox; D016678:Genome; D006801:Humans; D020407:Internet; D010802:Phylogeny; D011506:Proteins / Q000235:genetics; D012097:Repressor Proteins / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software; D014714:Vertebrates / Q000235:genetics; D051153:Wnt Proteins / Q000737:chemistry
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D011506:Proteins; D012097:Repressor Proteins; D051153:Wnt Proteins