BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions by Patrick Kück & Torsten H. Struck instant download

BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions by Patrick Kück & Torsten H. Struck instant download

abstractArticle history:BaCoCa (BAse COmposition CAlculator) is a user-friendly software that combines multiple statisticalReceived 4 July 2013approaches (like RCFV and C value calculations) to identify biases in aligned sequence data which potenRevised 12 September 2013tially mislead phylogenetic reconstructions. As a result of its speed and flexibility, the program providesAccepted 14 September 2013the possibility to analyze hundreds of pre-defined gene partitions and taxon subsets in one single processAvailable online 25 September 2013run. BaCoCa is command-line driven and can be easily integrated into automatic process pipelines of phyKeywords:logenomic studies. Moreover, given the tab-delimited output style the results can be easily used for further analyses in programs like Excel or statistical packages like R. A built-in option of BaCoCa is theSoftwaregeneration of heat maps with hierarchical clustering of certain results using R. As input files BaCoCaPhylogenomicscan handle FASTA and relaxed PHYLIP, which are commonly used in phylogenomic pipelines. BaCoCaRCFVis implemented in Perl and works on Windows PCs, Macs and Linux operating systems. The executableSaturationGC contentsource code as well as example test files and a detailed documentation of BaCoCa are freely availableInvariant positionsat . 2013 Elsevier Inc. All rights reserved.