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Bootstrap Analysis of Phylogenetic Sequences Using Maximum Parsimony

This script processes all PHYLIP-formatted aligned multiple sequence files in a specified directory to perform bootstrap analyses using maximum parsimony. Initially, aligned sequence files must be converted to PHYLIP format, with gaps replaced by "?" for accuracy. Files recommended for this analysis include A.fa, B.fa, alpha.fa, beta.fa, and atp_all.phy. Ultimately, the analysis aims to determine if resolution improves when a more closely related subgroup is examined independently of an outgroup.

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Bootstrap Analysis of Phylogenetic Sequences Using Maximum Parsimony

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  1. Home work assignment (due 4/6/2014) • Write a script that takes all phylipformated aligned multiple sequence files present in a directory, and performesa bootstrap analyses using maximum parsimony. • Files you might want to use are A.fa, B.fa, alpha.fa, beta.fafrom last week’s assignment, and atp_all.phy. BUT you first have to align them and convert them to phylipformat* AND you should replace gaps with “?” • (In the end you would be able to answer the question • “does the resolution increase if a more related subgroup is • analyzed independent from an outgroup?) • clustalw2 is one program frequently used to convert formats • system("clustalw -infile=$file.fa -align -output=PHYLIP");

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