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. .. rubric:: Parameters .. tabularcolumns:: column spec ================ ======================================================================== 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. ---------------- ------------------------------------------------------------------------ threads Type:{ **int**, **AUTO** } | Default: **1** Number of cores required for running IQ-TREE. ---------------- ------------------------------------------------------------------------ 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: **trimal** 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. .. code-block:: python [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 threads = 1 tree_software = (iqtree,fasttree) model = MFP trimming = trimal minimum = 4 delete_detail = true .. rubric:: Quick start After the parameters are modified properly, then run ``wgdi -at total.conf`` .. rubric:: Example The original results are easily accessible at `wgdi-example `_