I used Popart and TCS to make haplotype networks with mitochondrial DNA.
I used the "TCS Network" option on Popart, and both the options "gaps =5th state" and "gaps=missing" on TCS.
The topologies I found are differents : TCS found 3 more haplotypes than Popart.
Any explanation?
My alignment is 621 pb long and I have 133 sequences. Some of them have missing data especially at the very beginning and very end, could it be the reason why TCS doesn give me the same number of haplotypes than Popart ?
I set TCS at a 95% threshold, and I tried with both the options "Gaps = 5th state" and "gaps = missing", but the output is the same.
DNAsp gives me 7 haplotypes, which is consistent with Popart, but not TCS.
This does not add up. Both programs should recover the same number of haplotypes. i would run these data through a program like arlequin to establish how many haplotypes there are. Might as well compute a minimum spanning network while you are at it!
I ran Arlequin, and I finally found out the difference was due to missing data on informative sites. Thanks !
Yes, I am note that PopART masks any columns in your alignment with gaps or ambiguous characters, so you may have sequences that aren't truly identical that become identical after these columns are removed
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