Exceptional evolutionary lability of flower-like inflorescences (pseudanthia) in Apiaceae subfamily Apioideae
Description
A NEXUS file containing: 1) Aligned matrices of five molecular markers: nrDNA ITS (ITS), nr DNA ETS (ETS), rpoC1 (rpoC1), rps16 (rps16) and rpl16 (rpl16) 2) Aligned matrices of five molecular markers trimmed with TrimAl v. 1.259: nrDNA ITS (ITStrimmed), nr DNA ETS (ETStrimmed), rpoC1 (rpoC1trimmed), rps16 (rps16trimmed) and rpl16 (rpl16trimmed) 3) Concatenated trimmed matrices (CONCATENATED) 4) Maximum-likelihood tree reconstructed based on concatenated matrix with maximum-likelihood approach, as implemented in RAxML
Files
Steps to reproduce
Alignment trimming with TrimAl 1.259 (http://trimal.cgenomics.org/): trimal -in [input file] -out [output file.fas] -fasta -htmlout [output file.html] -automated1 Phylogeny reconstruction with RAxML 8.2.4 (https://cme.h-its.org/exelixis/web/software/raxml/): for bootstrap: raxmlHPC-PTHREADS-SSE3 -f a -p 22547 -s [input sequences] -m GTRGAMMA -x 15315 -# 1000 -t [input tree] -n [output file] -q [partition file] -T 20 for SH-like: raxmlHPC-PTHREADS-SSE3 -f J -p 22547 -s [input sequences] -m GTRGAMMA -t [input tree] -n [output file] -q [partition file] -T 16