Input - sungsik-kong/PhyNEST.jl GitHub Wiki

Input

In terminal, browse to the desired working directory using cd, for example. In the working directory, clone PhyNEST github wiki locally by typing:

git clone https://github.com/sungsik-kong/PhyNEST.jl.wiki.git

A new folder named PhyNEST.jl.wiki that contains tutorial markdown and other relevant files is cloned in the working directory. Move into the folder at PhyNEST.jl.wiki/example-data using, for example:

cd PhyNEST.jl.wiki/example-data/

:warning: Current version of PhyNEST requires input sequence alignment to be in sequential PHYLIP format, that looks something like:

4 30
outgroup ACCCTCGCTAGCGCTGGCTCGCGCCCGCGC
species_1 ACACTCGCTAGGGGGGGCTCGCGCTTGCGC
species_2 ACCCTCGCTAGCGCTTGCTTGCTCGCGCAC
species_3 AGCCTCGCTAGCGCTTGCTTGCTCCCGCAC

Multiple sequence alignment in a sequential PHYLIP format contains two sections: (1) a header (line 1) that describes the dimensions of the alignment (i.e., number of sequences and sequence length of the alignment) and (2) multiple sequence alignment itself (line 2 and onward).

:bangbang: PhyNEST requires the input alignment to contain four or more sequences. PhyNEST further assumes that each line in the input alignment (except for the first line) only contains sequence name and the sequence. Sequence name should not contain any space. Also, the sequence name and the corresponding sequence is separated by a single tab or a space.

Next: Example input data