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Build RaxML Trees and Clean Up


Teaching: 0 min
Exercises: 0 min
  • Key question (FIXME)

  • First learning objective. (FIXME)

Build a phylogenetic tree using RAxML

Warning: Threads

Do not use more threads (-T option) than available processors. Typically no more than 4 on a laptop and potentially many more on a cluster. NOTE: you can add a backbone constraint tree with the option -g. This should be done if clades within your group are always monophyletic in the literature (e.g. in phylogenomic or multigene analyses), but are not monophyletic in 18S trees. The sequences (tips) in this constraint tree must be in your alignment (they should be a subset of your sequences), and the names must match exactly.

raxmlHPC-PTHREADS-SSE3 -T 4 -m GTRCAT -c 25 -p 31415 -x 20398 -d -f a -N 100 -n NAME -s current_DB.trim.fasta –w /full/path/to/output_directory

Alternative: Build tree using FastTree

FastTree is very easy to install and gives you “quick and dirty” tree, in case you don’t want to or can’t wait for RAxML tree or in cases when the number of taxa is too high (more than several thousand).

fasttreeMP -gtr -nt current_DB.trim.fasta > NAME_fasttree.tre

Key Points

  • First key point. Brief Answer to questions. (FIXME)