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Repository mothur_phylo_diversity

Name: mothur_phylo_diversity

Owner: iuc

Synopsis: Wrapper for mothur application: Phylo.diversity.

Detailed description:

The mothur project seeks to offers a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more.
In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools.

Content homepage: https://www.mothur.org

Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur

Link to this repository: https://toolshed.g2.bx.psu.edu/view/iuc/mothur_phylo_diversity/5a9bf07c250c

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/mothur_phylo_diversity

Type: unrestricted

Revision: 11:5a9bf07c250c

This revision can be installed: True

Times cloned / installed: 2235

Repository README files - may contain important installation or license information

Readme files

Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)

The Mothur Tool Suite repository:
- Provides Mothur wrappers for the Mothur tools
- Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system

Installing Tools via the API:
This is a rather large tool suite, if you are having problems installing via the toolshed, try using the API instead
    - Install ephemeris: pip install ephemeris -U
    - Use ephemeris to install tools: shed_install -a <your admin API key> -t tools.yaml
    - (You can find a tools.yaml you can use in this repo as well)

Installing reference data from silva and greengenes:
    - There is a Galaxy datamanager for available for Mothur

RDP reference file (modified for mothur):
  http://www.mothur.org/wiki/RDP_reference_files
   - 16S rRNA reference (RDP): A collection of 9,662 bacterial and 384 archaeal 16S rRNA gene sequences with an improved taxonomy compared to version 6.
     http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
   - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
     http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
   - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
     http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
Silva reference:
  http://www.mothur.org/wiki/Silva_reference_files
  - Bacterial references (14,956 sequences)
    http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
  - Archaeal references (2,297 sequences)
    http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
  - Eukaryotic references (1,238 sequences)
    http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
  - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
    http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
Alignment database rRNA gene sequences:
  http://www.mothur.org/wiki/Alignment_database
  - greengenes reference alignment
    http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
  - SILVA (Silva reference)
    http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
Secondary structure mapping files:
  http://www.mothur.org/wiki/Secondary_structure_map
    http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
    http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
Lane masks:
  http://www.mothur.org/wiki/Lane_mask
  greengenes-compatible mask:
     - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
       http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
     - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
       http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
     - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
       http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
  SILVA-compatible mask:
     - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
       http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
Lookup Files for sff flow analysis using shhh.flows:
  http://www.mothur.org/wiki/Alignment_database

Name	Description	Version	Minimum Galaxy Version
Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Phylo.diversity View tool metadata	Alpha Diversity calculates unique branch length	1.39.5.0	16.07