What Are The Softwares To Infer The Derived Or Ancestral State Of Polymorphic Sites ?

Question

[Bioch'Ti]

Hi, I'm looking for a method/software to infer the ancestral or derived state of polymorphic sites using DNA alignments (in fasta format). For example, I have already identified thousands of orthologs between three plant species and aligned them (one species and two outgroups). Now, I would like to use these data to create unfolded site frequency spectrum. Are you aware of any software or script able to perform tho determine the ancestral or derived state of polymorphic sites? Thanks for your replies !

Answer 1

[Joseph Hughes]

PAUP and MESQUITE can be used for reconstructing the ancestral states on nodes of a phylogeny whether these are morphological characters or amino acids/nucleotides at particular sites.