Here you can find a very useful conda cheat-sheet.https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf
BASH - included natively in all Mac OS X and Linux distributions
You should type conda install -c bioconda package.
T-coffe
MAFFT
gblocks
IQ-TREE
MrBayes
EMBOSS
pal2nal
PAML
In the beginning we need to choose the group whose phylogeny will be inferred and the loci we will use for inferring their phylogeny. I suggest a lineage of animals and some mitochondrial markers, for which a lot of data are available. It is possible that you will need to refine your choice after checking about data availability. On NCBI select “Nucleotide” from the drop-down menu at the top and use the group and the gene names as queries. For a set of fifteen/twenty species of the group of interest you should download two /three gene sequences which are available for the most of them. Possibly, it would be interesting to have a PCG and a ncRNA. When you decide to download a given sequence, you have to place it in a FASTA-formatted file. Please ensure that the sequence names are the same in the two files, otherwise the subsequent step of concatenation will not work. Finally, you have to select outgroup sequences. You can find an example of a starting file here.