Lab 3 - Distance analysis with PHYLIP, and FastME

In this lab we will learn about three phylogenetic programs that can be used for distance analysis

Prerequisites:

Login to Nova cluster

# Login
ssh yourname@nova.its.iastate.edu
# Also, request a core for yourself
salloc -p class-long -N 1 -n 1 -t 2:00:00 -A s2023.eeob.563.1

Update your EEOB563-Spring2023 git repository

• Go to the repository and pull the updates: git pull origin master

Accessing the programs

• Both Phylip and FastME are installed as a modules on Nova (load with module load phylip and module load fastme). You can also install them from their websites (see links page)
• Online version of fastme is also available, but you should avoid it to practice your command line skills.

EMBOSS package

EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. It can be loaded as a module module load emboss or used online. Among its many programs, you may be particularly interested in seqret, which does sequence conversion among various formats. Here are a couple of examples:

### convert fasta alignment to nexus
seqret -sequence <input.fa> -outseq <output.nex> -osformat nexus/nexusnon
### convert fasta alignment to phylip
seqret -sequence <input.fa> -outseq <output.nex> -osformat phylip/phylipnon

Lab tutorial

Lab 3: PHYLIP, and FastME

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