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'

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 Type
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

Version History

Version 1 (earliest) Created 6th Jun 2022 at 15:14 by Miguel Roncoroni

Initial commit


Open master 02ae460
help Creators and Submitter
Creators
Not specified
Additional credit

Miguel Roncoroni

Submitter
Activity

Views: 97

Created: 6th Jun 2022 at 15:14

Last used: 29th Jun 2022 at 04:48

help Attributions

None

Total size: 21.4 KB
Powered by
(v.1.12.0)
Copyright © 2008 - 2022 The University of Manchester and HITS gGmbH

By continuing to use this site you agree to the use of cookies