![]() RAxML is conservative (which is a better way to do it). Note that different programs likely treat missing data and indels differently. A simpler way is to run the file in RAxML which will automatically create a reduced alignment with only unique samples (which can be converted back to fasta format using ruby). One way to reduce the dataset to haplotypes is to open the fasta version of the file in BioEdit and simply go through and remove any samples that are identical (based on the nj tree). I usually print an nj tree from MEGA with all individuals included. In MacClade though you have to select the option that preserves the original sequence names. ![]() The few program I have tried this in (except MacClade) renames all of your sequences, thus making it difficult to know what they were originally. MacClade comes close, but only runs on a Mac so I don't have easy access to it. I have never found a simple method that I like for doing this. ![]() ![]() What follows is not the quickest, nor simplest way of doing this and it involves a lot of manual editing (which makes it prone to errors). How to make a haplotype table and dataset? How to make a haplotype table and dataset? ![]()
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