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
  • 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

Version History

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

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Frozen Version-1 02ae460
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Miguel Roncoroni

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Views: 1714

Created: 6th Jun 2022 at 15:14

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