Paralog alignments

Below are links to the paralog alignments used in the last and most stringent stage of analysis. Each is an alignment five homologs: a methanogen ORF & its paralog, an E. coli ORF & its paralog, and a cyanobacterial ORF.

These alignments were created by individually aligning each of the first four sequences to the last seqeunce and then using the last sequence as the guide to make the multiple seqeunce alignment. The pairwise alignments were created by a modified Needleman-Wunsch algorithm using the BLOSUM62 amino acid substitution matrix, a gap opening penalty of 7, a gap extension penalty of 2, and by penalizing end gaps 0.3 times as much as a gap of the same length in the middle.
 

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