Houses a snakemake workflow used for multiple sequence alignment and maximum likelihood phylogeny construction of genes or proteins. Originally used to study sex determination genes in mosquitoes.

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snakemake-alignment_phylogeny — View Workflow

Snakemake file

This snakemake file contains a workflow allowing the creation of MAFFT alignments and RAxML phylogenies. Inputs can either be a set of amino acid or nucleotide sequences. It is coded for use with a snakemake configuration by RomainFeron , so that it works with a computing cluster managed by SLURM. Note that the outgroups in the ProteinTree and GeneTree rules need to be changed to accomodate your dataset.

Dataset

Contains the amino acid and CDS sequences of the sex determination gene doublesex in Aedes aegypti, Drosophila melanogaster and 13 Anopheles species. Male and female transcripts are present within each. This was the original dataset the workflow was tested on when I made it.

Code Snippets

shell:
    "source /dcsrsoft/spack/bin/setup_dcsrsoft;"
    "module load gcc/8.3.0;"
    "module load mafft/7.453;"
    "mafft --maxiterate 100 --globalpair --clustalout {input} > GenesAlignments/{wildcards.gene}Gclus.aln;"

SnakeMake MAFFT API (EBI) From line 10 of main/Snakefile

shell:
    "source /dcsrsoft/spack/bin/setup_dcsrsoft;"
    "module load gcc/8.3.0;"
    "module load mafft/7.453;"
    "mafft --maxiterate 100 --globalpair {input} > GenesAlignments/{wildcards.gene}Gfas.aln;"

SnakeMake MAFFT API (EBI) From line 25 of main/Snakefile

shell:
    "module load Bioinformatics/Software/vital-it;"
    "module add SequenceAnalysis/Filtering/trimAl/1.4.1;"
    "module load SequenceAnalysis/Filtering/trimAl/1.4.1;"
    "trimal -in {input} -out {wildcards.gene}Gtrimmedfas.aln -htmlout {wildcards.gene}Gtrimmedfas.html -automated1;"
    "mv *trimmed* /users/jtan/scratch/jtan/1ststep/dsx/GenesAlignmentsTrimmed/;"
    "cd ..;"

SnakeMake trimAl From line 41 of main/Snakefile

shell:
    "module load Bioinformatics/Software/vital-it;"
    "module add Phylogeny/raxml/8.2.12;"
    "module load Phylogeny/raxml/8.2.12;"
    "cd GenesAlignmentsTrimmed;"
    "rm -r /users/jtan/scratch/jtan/1ststep/dsx/GenesTrees/{wildcards.gene}GTree/;"
    "mkdir /users/jtan/scratch/jtan/1ststep/dsx/GenesTrees/{wildcards.gene}GTree/;"
    "raxmlHPC -d -s {wildcards.gene}Gtrimmedfas.aln -n {wildcards.gene}GTree -m GTRGAMMA -x 10 -p 10 -# autoMR -f a -o Dmel_Female -w /users/jtan/scratch/jtan/1ststep/dsx/GenesTrees/{wildcards.gene}GTree/"

SnakeMake raxml-ng From line 62 of main/Snakefile

shell:
    "source /dcsrsoft/spack/bin/setup_dcsrsoft;"
    "module load gcc/8.3.0;"
    "module load mafft/7.453;"
    "mafft --maxiterate 100 --globalpair --clustalout {input} > GenesAlignments/{wildcards.gene}Pclus.aln;"

SnakeMake MAFFT API (EBI) From line 80 of main/Snakefile

shell:
    "source /dcsrsoft/spack/bin/setup_dcsrsoft;"
    "module load gcc/8.3.0;"
    "module load mafft/7.453;"
    "mafft --maxiterate 100 --globalpair {input} > GenesAlignments/{wildcards.gene}Pclus.aln;"

SnakeMake MAFFT API (EBI) From line 94 of main/Snakefile

shell:
    "module load Bioinformatics/Software/vital-it;"
    "module add SequenceAnalysis/Filtering/trimAl/1.4.1;"
    "module load SequenceAnalysis/Filtering/trimAl/1.4.1;"
    "trimal -in {input} -out {wildcards.gene}Ptrimmedfas.aln -htmlout {wildcards.gene}Ptrimmedfas.html -automated1;"
    "mv *trimmed* /users/jtan/scratch/jtan/1ststep/dsx/ProteinsAlignmentsTrimmed/;"
    "cd ..;"

SnakeMake trimAl From line 110 of main/Snakefile

shell:
    "cd ProteinsAlignmentsTrimmed;"
    "module load Bioinformatics/Software/vital-it;"
    "module add Phylogeny/raxml/8.2.12;"
    "module load Phylogeny/raxml/8.2.12;"
    "rm -r /users/jtan/scratch/jtan/1ststep/dsx/ProteinsTrees/{wildcards.gene}PTree/;"
    "mkdir /users/jtan/scratch/jtan/1ststep/dsx/ProteinsTrees/{wildcards.gene}PTree/;"
    "raxmlHPC -d -s {wildcards.gene}Ptrimmedfas.aln -n {wildcards.gene}PTree -m PROTGAMMAJTTF -x 10 -p 10 -# autoMR -f a -o Dmel_Female -w /users/jtan/scratch/jtan/1ststep/dsx/ProteinsTrees/{wildcards.gene}PTree/;"