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I am working on success rate of DNA barcoding in identification of species using distance and tree based methods.

Regarding distance based method, I have used Adhoc and species identifier and confirmed species identification using best closest match criteria (BCM).

Please suggest program/software/method for tree based identification (using NJ, parsimony, bayes), exhibiting clustering (number of clusters formed for particular species) that will suggest singleton (=Ambigious) species.

(For more details: Attached image) (Please Note: It is not possible to do it manually as iam having >4000 specimens)

Answers detailing methods or softwares appereciated! Thank you!

enter image description here

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Are you searching for something like this: en.wikipedia.org/wiki/List_of_phylogenetics_software this post is some what off topic. –  Devashish Das Jul 15 at 5:56
    
@Devashish Das, thank you for your reply, to make it more clear, ive attached image. Pls have a look, keep posting. –  Rahul Jul 15 at 6:13
    
You can try PHYLIP and ClustalW. You can run them from commandline and this can be automated. –  WYSIWYG Jul 18 at 12:53

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