Steps.txt

Note:The conda environment "SANIBEL" has install all packages below.

1. create and activate a conda environment
2. install dependencies
### replace conda with mamba to install all packages
#$mamba install perl-time-piece 
1. $mamba install perl-bioperl
2. $mamba install samtools
3. $mamba install bcftools
4. $mamba install mummer
5. $mamba install bowtie2
6. $mamba install fasttree
7. $mamba install bbmap
8. $mamba install raxml
9. $mamba install perl-parallel-forkmanager
10. $mamba install perl-statistics-distributions
11. $mamba install paml
12. $mamba install mafft
13. $amba install hyphy

3. Download PhaME

4. Go to PhaME top directory. In the top directory, you should find the folder "test", "src", etc.

5. Create the folder "workdirs" and "/workdirs/mytest". For example: $mkdir -p ./test/workdirs/mytest

6. Copy your data to /workdirs/mytest/

7. Create a new control file and set all parameters in it. For example: a control file "test/ctl_files/mytest3.ctl"

8. Run the command phame in the folder "src". For example: $perl src/phame test/ctl_files/mytest3.ctl

Note: Candida fungi test showed that only fasta data works, while its fastq data from PacBio long sequencing do not work. Possible reason is that PhaME only handle paired/single reads from Illumina.