fastcodeml_docker

fastcodeml inside a docker container

installation

you can download the docker container for 1.3.0 or 1.1.0:

1.3.0 version:

sudo docker run -i -t --entrypoint /bin/bash philippmuench/fastcodeml

1.1.0 version:

sudo docker run -i -t --entrypoint /bin/bash philippmuench/fastcodeml:1.1.0

you can mount your data to the docker container e.g. by using

sudo docker run -v my_data_folder:/data -i -t --entrypoint /bin/bash philippmuench/fastcodeml

then you can access your data inside the docker container in the /data folder

usuage

input codon alignment data must be in phylip format (e.g. pal2nal output) input tree must be in newick format

for v.1.3.0: fast -m 22 -bl -nt 1 -hy 0 data/tree.nwk data/msa.phy

for v.1.1.0: fast -m 22 -bf -hy 0 data/tree.nwk data/msa.phy