ML phylogenetic reconstruction
Version 1

Workflow Type: Galaxy

Phylogenetic reconstruction using genome-wide and single-gene alignment data. Here we use maximum likelihood reconstruction program IQTree. Data can be prepared using the phylogenetic data preparation workflow prior to phylogenetic reconstruction. Resulting trees can be viewed interactively using Galaxy's 'Phyloviz' or 'Phylogenetic Tree Visualization'

SEEK ID: https://workflowhub.eu/workflows/359?version=1

Inputs

ID	Name	Description	Type
Input alignment collection	Input alignment collection	n/a	n/a
general_options	general_options	runtime parameter for tool IQ-TREE	n/a
general_options	general_options	runtime parameter for tool IQ-TREE	n/a
likelihood_mapping	likelihood_mapping	runtime parameter for tool IQ-TREE	n/a
general_options	general_options	runtime parameter for tool IQ-TREE	n/a
general_options	general_options	runtime parameter for tool IQ-TREE	n/a
likelihood_mapping	likelihood_mapping	runtime parameter for tool IQ-TREE	n/a

Steps

ID	Name	Description
0	Input alignment collection
1	IQ-TREE	toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.3
2	ClipKIT. Alignment trimming software for phylogenetics.	toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0
3	ASTRAL-III. Tool for estimating an unrooted species tree given a set of unrooted gene trees.	toolshed.g2.bx.psu.edu/repos/padge/astral/astral/0.1.0
4	PhyKit - Alignment-based functions	toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0
5	IQ-TREE	toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.3

Outputs

ID	Name	Description
bionj	bionj	n/a
treefile	treefile	n/a
contree	contree	n/a
mldist	mldist	n/a
splits.nex	splits.nex	n/a
iqtree	iqtree	n/a
trimmed_output	trimmed_output	n/a
log_output	log_output	n/a
output	output	n/a
log_output	log_output	n/a
fasta	fasta	n/a
partition	partition	n/a
occupancy	occupancy	n/a
bionj	bionj	n/a
treefile	treefile	n/a
contree	contree	n/a
mldist	mldist	n/a
splits.nex	splits.nex	n/a
iqtree	iqtree	n/a