Mercurial > repos > earlhaminst > geneseqtofamily

annotate readme.md @ 6:266800d51605 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 3dbeddc06c9d15aadcc66a7eb7376c29da9233a3"
author earlhaminst
date Thu, 10 Jun 2021 16:18:59 +0000
parents 06470b2e491f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
1 # GeneSeqToFamily: the Ensembl GeneTrees pipeline as a Galaxy workflow
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
2
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
3
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
4 ## Introduction
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
5
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
6 GeneSeqToFamily is an open-source Galaxy workflow based on the [Ensembl GeneTrees](http://www.ensembl.org/info/genome/compara/homology_method.html) pipeline. The Ensembl GeneTrees pipeline [1] infers the evolutionary history of gene families, represented as gene trees. It is a computational pipeline that comprises clustering, multiple sequence alignment, and tree generation (using [TreeBeST](http://treesoft.sourceforge.net/treebest.shtml)), to discover familial relationship.
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
7
3
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
8 ## Installation
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
9
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
10 To use this workflow, please [install](https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/) the required tools (listed below) into Galaxy from the Galaxy ToolShed. Also [install and import](https://galaxyproject.org/toolshed/workflow-sharing/#finding-workflows-in-toolshed-repositories) the workflow from the Galaxy ToolShed.
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
11
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
12 ### List of required tools
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
13 The 3 workflows in this repository requires Galaxy tools from the following ToolShed repositories:
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
14
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
15 * [emboss_5](https://toolshed.g2.bx.psu.edu/view/devteam/emboss_5/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
16 * [ncbi_blast_plus](https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
17 * [blast_parser](https://toolshed.g2.bx.psu.edu/view/earlhaminst/blast_parser/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
18 * [hcluster_sg](https://toolshed.g2.bx.psu.edu/view/earlhaminst/hcluster_sg/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
19 * [hcluster_sg_parser](https://toolshed.g2.bx.psu.edu/view/earlhaminst/hcluster_sg_parser/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
20 * [t_coffee](https://toolshed.g2.bx.psu.edu/view/earlhaminst/t_coffee/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
21 * [filter_by_fasta_ids](https://toolshed.g2.bx.psu.edu/view/galaxyp/filter_by_fasta_ids/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
22 * [treebest_best](https://toolshed.g2.bx.psu.edu/view/earlhaminst/treebest_best)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
23 * [gafa](https://toolshed.g2.bx.psu.edu/view/earlhaminst/gafa/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
24 * [fasta_to_tabular](https://toolshed.g2.bx.psu.edu/view/devteam/fasta_to_tabular/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
25 * [text_processing](https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
26 * [uniprot_rest_interface](https://toolshed.g2.bx.psu.edu/view/bgruening/uniprot_rest_interface/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
27 * [suite_ensembl_rest](https://toolshed.g2.bx.psu.edu/view/earlhaminst/suite_ensembl_rest/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
28
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
29 Helper tools for data preparation:
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
30
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
31 * [ensembl_longest_cds_per_gene](https://toolshed.g2.bx.psu.edu/view/earlhaminst/ensembl_longest_cds_per_gene/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
32 * [ete](https://toolshed.g2.bx.psu.edu/view/earlhaminst/ete/)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
33 * [gstf_preparation](https://toolshed.g2.bx.psu.edu/view/earlhaminst/gstf_preparation/) - to convert gene feature files from GFF3 and/or JSON format to SQLite and format CDS sequence headers
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
34
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
35
0
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
36 ## Workflow inputs and steps
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
37
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
38 ### Inputs
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
39 GeneSeqToFamily requires the following inputs:
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
40
3
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
41 * the coding sequences (CDS) in FASTA format (this can be achieved with GeneSeqToFamily preparation tool)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
42 * gene feature information in SQLite format (this can be achieved with GeneSeqToFamily preparation tool)
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
43 * a species tree in Newick format (this can be generated by ete tool in Galaxy)
0
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
44
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
45 ### Steps
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
46
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
47 The pipeline is made up of 7 main steps:
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
48
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
49 1. Translation of CDS to protein sequences
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
50 2. All-vs-all BLASTP of protein sequences
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
51 3. Cluster protein sequences using [hcluster_sg](https://github.com/douglasgscofield/hcluster) and BLASTP scores
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
52 4. Multiple sequence alignment (MSA) for each cluster using [T-Coffee](http://www.tcoffee.org/Projects/tcoffee/)
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
53 5. Generate gene trees from MSAs using [TreeBeST](http://treesoft.sourceforge.net/treebest.shtml)
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
54 6. Create an SQLite database from the MSAs, gene trees and gene feature information using Gene Alignment and Family Aggregator (GAFA)
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
55 7. Visualise the GAFA dataset using Aequatus
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
56
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
57
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
58 ### Helper tools:
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
59
3
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
60 We have developed various tools to help with data preparation for the workflow. This includes tools for retrieving sequences, and features from Ensembl using its REST API, and tools to parse Ensembl results into the required formats for the workflow. We also developed a tool to merge gene feature files and convert them from GFF3 (Gene Feature File) and/or JSON format to SQLite, which is then used to generate the Aequatus dataset.
0
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
61
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
62
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
63 ## Results
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
64
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
65 The resulting gene families can be visualised using the [Aequatus.js](https://github.com/TGAC/aequatus.js) interactive tool, which is developed as part of the [Aequatus software](https://github.com/TGAC/aequatus) [2].
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
66
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
67 The Aequatus.js plugin provides an interactive visual representation of the phylogenetic and structural relationships among the homologous genes, using a shared colour scheme for coding regions to represent homology in internal gene structure alongside their corresponding gene trees. It is also able to indicate insertions and deletions in homologous genes with respect to shared ancestors.
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
68
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
69
5
06470b2e491f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 2c7c545579169dda723cd7d91d9ccef1c5061fed
earlhaminst
parents: 3
diff changeset
70 ## Citation information:
06470b2e491f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 2c7c545579169dda723cd7d91d9ccef1c5061fed
earlhaminst
parents: 3
diff changeset
71
06470b2e491f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 2c7c545579169dda723cd7d91d9ccef1c5061fed
earlhaminst
parents: 3
diff changeset
72 If you are using GeneSeqToFamily for any kind of research purpose, please cite the following paper:
06470b2e491f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 2c7c545579169dda723cd7d91d9ccef1c5061fed
earlhaminst
parents: 3
diff changeset
73
06470b2e491f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 2c7c545579169dda723cd7d91d9ccef1c5061fed
earlhaminst
parents: 3
diff changeset
74 Anil S. Thanki, Nicola Soranzo, Wilfried Haerty, Robert P. Davey (2018) [GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline](https://doi.org/10.1093/gigascience/giy005) *GigaScience* 7(3), giy005, doi: 10.1093/gigascience/giy005
0
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
75
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
76
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
77 ## References
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
78
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
79 1. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E (2009) [EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.](http://genome.cshlp.org/content/19/2/327) *Genome Res.* 19(2):327–335, doi: 10.1101/gr.073585.107
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
80 2. Thanki AS, Ayling S, Herrero J, Davey RP (2016) [Aequatus: An open-source homology browser.](http://biorxiv.org/content/early/2016/06/01/055632) *bioRxiv*, doi: 10.1101/055632
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
81
3
fd620c523d63 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 588282bf5cbb9909ad9cd8c316ec33158c858727
earlhaminst
parents: 0
diff changeset
82
0
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
83 ## Project contacts:
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
84
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
85 * Anil Thanki <Anil.Thanki@earlham.ac.uk>
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
86 * Nicola Soranzo <Nicola.Soranzo@earlham.ac.uk>
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
87 * Robert Davey <Robert.Davey@earlham.ac.uk>
b92f5ab6d127 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 9c148d5ba49d9de5f7b1c1f4b32cd8b5e56cb975-dirty
earlhaminst
parents:
diff changeset
88
5
06470b2e491f planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 2c7c545579169dda723cd7d91d9ccef1c5061fed
earlhaminst
parents: 3
diff changeset
89 Copyright &copy; 2016-2018 Earlham Institute, Norwich, UK