Sir, Hope this mail will find you in sound. I was trying to align 13 apicomplexan genome using mauve. I got 6 outputs (attached without the alignment file; its too large 297 mb and it may not necessary for current discussion, I can provide if you think it is needed). My objective is to create a phylogenetic tree using the alignment. Is it possible? I converted the alignment to standard fasta format (attached) then to nexus and phylip format for raxml and mrbayes. Everything seems ok. But the problem is my alignment file contains 39 sequence which indicates I have exactly three alignments inside one big alignment file. My question is, why I am getting 39 sequence instead of 13? How can I use this alignment? Can I split it into 3 individual fasta file and then convert them into phylip or nexus? Thanks in advance. Best Regards Zillur Rahman Phd Student at Bioinformatics Lab University of Puerto Rico, Rio-Piedras
mauve_out_test.tar.gz
Description: GNU Zip compressed data
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