Alignmenttrees

Phylogenetic tree construction using alignment or collinear genes. A phylogenetic tree is constructed for gene sets that each row of the alignment file during this process. By using ASTRAL merge, you can obtain a multispecies or subgenomes coalescent tree.

Parameters

Parameters	Standards and instructions
alignment	Type: file | Default: - The merged file of multiple alignment files with the same reference.
gff	Type: file | Default: - Gff of reference, If alignment has no reference species, delete it.
lens	Type: file | Default: - lens of reference, If alignment has no reference species, delete it.
dir	Type: folder | Default: - Folder for phylogenetic trees.
sequence_file	Type: file | Default: - In general, it is protein sequences (pep), if it is coding sequences (cds), cds_file need to be deleted.
cds_file	Type: file | Default: none It is required when the method of constructing trees involvesv codon. Otherwise, it can be discarded.
codon_positon	Type:str | Default: 1,2,3 1,2 mean codon1&2; 1,2,3 mean no codon removed.
trees_file	Type: file | Default: - Merge multiple nwk-format tree files.
align_software	Type:{ muscle, mafft } | Default: muscle Software of multiple sequence alignment.
tree_software	Type:{ iqtree, fasttree } | Default: iqtree Software of constructing phylogenetic trees.
model	Type: str | Default: - Merge multiple nwk-format tree files.
trimming	Type:{ trimal, divvier} | Default: none Software of removal of spurious sequences.
minimum	Type: int | Default: 4 Minimum number of gene sets in constructing phylogenetic tree.
delete_detail	Type: bool | Default: false Whether or not to keep intermediate files when constructing phylogenetic tree.

Use command to enter the folder wgdi -at ? >> total.conf Take out the parameter file. Afterwards, use the ASTRAL command java -jar /path/astral.5.7.7.jar -i trees_file.nwk -o out.tre -t 8, you can obtain a multispecies or subgenomes coalescent tree.

[alignmenttrees]
alignment = alignment file (.csv)
gff = gff file (reference genome, If alignment has no reference species, delete it)
lens = lens file (If alignment has no reference species, delete it)
dir = output folder
sequence_file = sequence file (.fa)
cds_file = cds file (.fa)
codon_positon = 1,2,3  (1,2 mean codon1&2; 1,2,3 mean no codon removed)
trees_file =  trees (.nwk)
align_software = mafft
tree_software =  (iqtree,fasttree)
model = MFP
trimming =  trimal
minimum = 4
delete_detail = true

Quick start

After the parameters are modified properly, then run wgdi -at total.conf

Example

The original results are easily accessible at wgdi-example