Perform phylogenetic analyses using command line on Mac

Downhill to the ocean (Kuchinoshima Island, 2018).

When you perform a phylogenetic analysis, you may use MEGA which is a quite convenient software. But it does not work properly on Mac. Moreover, we sometimes forget how we made the phylogenetic tree.

Here, I keep a record of how I perform phylogenetic analyses using command line.

This is just a log of my trial and error. I DO NOT guarantee the proper functioning of codes below.

1. Maximum likelihood

Use RAxML-NG and Modeltest-NG.

brew tap brewsci/bio

brew install raxml-ng

brew install git cmake libtool automake

git clone --recursive https://github.com/ddarriba/modeltest

cd modeltest

mkdir build && cd build

cmake ..

make

Select a substitution model.

modeltest-ng -i input.fas -o output

Then, you'll find an output.out file containing best substitution models under AIC, AICc, and BIC. Commands are also listed in the file.

Commands:

> raxml-ng --msa input.fas --model TPM1uf+I+G4

Just run the command.

raxml-ng --msa input.fas -all --model TPM1uf+I+G4 --redo --bs-trees 100 --threads 2

Open an input.fas.raxml.support file with FigTree. Bootstrap values for each node can be shown by selecting "label".

2. Neighbor joining

Convert file format; fasta to nexus. I used MEGA (it worked somehow). I modified data description: datatype=nucleotide to datatype=dna. There are other useful tools for the conversion.

Download MrModeltest2.

Make a symbolic links of MrModeltest2 and MrModelblock in a current directory.

ln -s /PATH/To/MrModeltest2/bin/macosx/mrmodeltest2.4.macos.10.13.3 .

ln -s /PATH/To/MrModeltest2/doc/MrModelblock .

Download PAUP.

Run PAUP.

paup4a166_osx

exe Fasta-All_fromAlam7.nexus;

exe MrModelblock;

mrmodel.scores will be generated.

Run MrModeltest2.

mrmodeltest2.4.macos.10.13.3 < mrmodel.scores > mrmodel.out

mrmodel.out will be generated which contains a PAUP* command block.

PAUP* Commands Block: If you want to implement the previous estimates as likelihod settings in PAUP*, attach the next block of commands after the data in your PAUP file:

Likelihood settings from best-fit model (GTR+I+G) selected by hLRT in MrModeltest 2.4

]

BEGIN PAUP;

Lset Base=(0.2646 0.3385 0.1237) Nst=6 Rmat=(2.882252693 16.924112320 1.114207029 0.802115560 11.847808838) Rates=gamma Shape=0.4257 Pinvar=0.4273;

END;

Run PAUP* using the commands.

paup4a166_osx

log file=nj.log

execute input.nexus;

set criterion=distance;

Lset Base=(0.2646 0.3385 0.1237) Nst=6 Rmat=(2.882252693 16.924112320 1.114207029 0.802115560 11.847808838) Rates=gamma Shape=0.4257 Pinvar=0.4273;

Bootstrap search=NJ nreps=1000 conLevel=50;

saveTrees from=1 to=1 file=nj.tre saveBootP=nodeLabels maxDecimals=1 replace=yes;

Open nj.tre with FigTree.