BaCoCa (Base Composition Calculator) is designed to perform multiple statistical analyses on multiple nucleotide and amino-acid sequence alignments. The results of the BaCoCa analyses can be used for a detailed and statistical comprehensive data evaluation. Furthermore, the results can help to identify phylogenetic sequence biases which can lead to incorrect tree reconstructions. The program can handle hundreds of user specified gene and taxon partitions of a single sequence input file in one process run. BaCoCa is a command-line driven program written in PERL and works on WindowsPCs, Macs and Linux operating systems. Therefore, it can be easily integrated into automatic pipeline processes of phylogenomic studies.