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HAL - a program for semi-automated phylogenomic analyses

The current version of Hal is a set of scripts written in PERL v5.8.4 that takes all versus all BLASP text output (from any number of proteomes) as input to identify orthologs, extract orthologous sequences and concatenate them into a super alignment. These steps are achieved by linking existing programs such as Tribe MCL and Clustal W with PERL scripts.


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