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	File[]

Steps

ID	Name	Description
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	Type
_anonymous_output_1	_anonymous_output_1	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
_anonymous_output_3	_anonymous_output_3	n/a	File
_anonymous_output_4	_anonymous_output_4	n/a	File
_anonymous_output_5	_anonymous_output_5	n/a	File
_anonymous_output_6	_anonymous_output_6	n/a	File
Trimmed alignment.	Trimmed alignment.	n/a	File
Output tree file	Output tree file	n/a	File
Astral log.	Astral log.	n/a	File
An occupancy file that summarizes the taxon occupancy per sequence	An occupancy file that summarizes the taxon occupancy per sequence	n/a	File
Concatenated fasta alignment file	Concatenated fasta alignment file	n/a	File
A partition file ready for input into RAxML or IQ-tree	A partition file ready for input into RAxML or IQ-tree	n/a	File
IQ-TREE on input dataset(s): BIONJ Tree	IQ-TREE on input dataset(s): BIONJ Tree	n/a	File
IQ-TREE on input dataset(s): MaxLikelihood Tree	IQ-TREE on input dataset(s): MaxLikelihood Tree	n/a	File
IQ-TREE on input dataset(s): Consensus Tree	IQ-TREE on input dataset(s): Consensus Tree	n/a	File
IQ-TREE on input dataset(s): MaxLikelihood Distance Matrix	IQ-TREE on input dataset(s): MaxLikelihood Distance Matrix	n/a	File
IQ-TREE on input dataset(s): Report and Final Tree	IQ-TREE on input dataset(s): Report and Final Tree	n/a	File
IQ-TREE on input dataset(s): Occurence Frequencies in Bootstrap Trees	IQ-TREE on input dataset(s): Occurence Frequencies in Bootstrap Trees	n/a	File