Computational protocol: Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species

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Protocol publication

[…] Phylogenetic relationships and divergence times for the plant species were estimated using the online software Phylomatic and the Branch Length Adjuster (BLADJ) algorithm in the Phylocom 4.2 software . Phylomatic matches taxon sample names with information on seed plant phylogeny according to Angiosperm Phylogeny Group III (source tree R20100701) to derive evolutionary relationships among samples. The BLADJ algorithm constrains the age of nodes included in the sample according to the dated molecular phylogeny of Wikström et al. , and for nodes where an age estimate is unavailable, sets the age as the midpoint between constrained nodes to produce an ultrametric topology. For the animal tree, relationships among phyla are as per the recent study of Dunn et al. , and were supplemented with information from finer scale studies including Arthropoda , Mollusca , Mammalia and Squamata . The animal tree was input into Phylocom and made ultrametric using minimum age constraints according to Benton and Donoghue as reported on the Date-a-Clade website (http://www.fossilrecord.net/dateaclade) and the BLADJ algorithm. The resulting phylogenetic trees ( and ) were drawn with the APE package within the R language . […]

Pipeline specifications

Software tools Phylomatic, Phylocom, APE
Application Phylogenetics