I'm looking for the most suitable pipeline to perform a whole-genome multiple sequence alignment (MSA) of around 1000 vertebrate species. The goal is to identify conserved elements (and yes, I need this number of species).
As far as I know, the maximum number of sequences used in publicly available whole-genome MSA of vertebrate species is 100 (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=multiz100way).
I'm new to MSA, so I would like to know which pipeline would be the most efficient in my case and how much time and computational resources may I need (I have a slurm cluster, so parallelization is preferred).
Would it be OK to perform MSA in batches of 100 sequences and then concatenate the results somehow?
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Thanks a lot! That's what I needed!