phylip

This repo contains the source code of phylip, written by Joe Felsenstein et al., and downloaded on January 8, 2021 from https://evolution.genetics.washington.edu/phylip/getme-new1.html .

Compiling

Generally builds on https://evolution.genetics.washington.edu/phylip/install.html .

docker run -it dunnlab/ubuntu-dev:20.04 /bin/bash
git clone https://github.com/dunnlab/phylip.git
cd phylip/phylip-3.697/src/
make -f Makefile.unx install
export PATH="/phylip/phylip-3.697/exe:$PATH"

Running

I include a few datasets

• test.phy is from the dnaml documetnation
• siph16s.phy is a quick siphonophore dataset I made
• alignment.phy is from this primer

To run a test datasets:

cd /phylip
dnaml

Then enter the name of the dataset.

Profile with gprof

Further reading

• The GNU Profiler
• How to read gprof output(pdf)

# in linux container dunnlab/ubuntu-dev
cd phylip-3.697/src
make --file=Makefile.unx dnaml
cd ../../
ln -s siph16s.phy infile
phylip-3.697/src/dnaml
gprof -b phylip-3.697/src/dnaml gmon.out
gprof phylip-3.697/src/dnaml gmon.out > gmon.txt