@article{PAR00002859,
  title = {{P}hylogeny.fr: robust phylogenetic analysis for the non-specialist},
  author = {{D}ereeper, {A}. and {G}uignon, {V}. and {B}lanc, {G}. and {A}udic, {S}. and {B}uffet, {S}. and {C}h{\'e}venet, {F}ran{\c{c}}ois and {D}ufayard, {J}.{F}. and {G}uindon, {S}. and {L}efort, {V}. and {L}escot, {M}. and {C}laverie, {J}.{M}. and {G}ascuel, {O}.},
  editor = {},
  language = {{ENG}},
  abstract = {{P}hylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. {T}he {P}hylogeny.fr platform transparently chains programs to automatically perform these tasks. {I}t is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. {P}hylogeny.fr offers three main modes. {T}he '{O}ne {C}lick' mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: {MUSCLE} for multiple alignment, {P}hy{ML} for tree building, and {T}ree{D}yn for tree rendering. {A}ll parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. {T}he '{A}dvanced' mode uses the same pipeline but allows the parameters of each program to be customized by users. {T}he '{A} la {C}arte' mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. {P}rior to phylogenetic analysis, users can also collect neighbors of a query sequence by running {BLAST} on general or specialized databases. {A} guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. {P}hylogeny.fr is available at: http://www.phylogeny.fr/},
  keywords = {},
  booktitle = {},
  journal = {{N}ucleic {A}cids {R}esearch},
  volume = {36 ({W}eb {S}erver issue)},
  numero = {},
  pages = {{W}465--{W}469},
  year = {2008},
  DOI = {10.1093/nar/gkn180},
  URL = {https://www.documentation.ird.fr/hor/{PAR}00002859},
}