Analysis/Pipeline_description.md

In TGuillerme/Inapp: Reconstruction of Inapplicable Discrete Characters on Phylogenetic Trees

Pipeline for testing the effect of inapplicable data

1 - Get the most parsimonious tree island in PAUP

Search for the most parsimonious tree island treating NAs as missing data and save all the topologies from the island and the score.

execute $MATRIX.nex
hsearch addseq=random nreps=1000
savetrees /file=$MATRIX.tre

Then combine both matrix and trees into $MATRIX.tre

2 - Calculate tree length of all the topologies in the island in PAUP and morphy

• First calculate the tree length treating NAs as an extra state in PAUP

execute $MATRIX.nex
Pscores /scorefile=$MATRIX.NAmiss.score
Pset GapMode=newstate
Pscores /scorefile=$MATRIX.NAextr.score

• Then calculate the tree length using the morphy algorithm

TGuillerme/Inapp documentation built on Feb. 4, 2024, 7:26 a.m.