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amanita_thiersii

Code and data for A. thiersii project

https://github.com/noramushrooms/amanita_thiersii

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (3.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Code and data for A. thiersii project

Basic Info
  • Host: GitHub
  • Owner: noramushrooms
  • Default Branch: main
  • Size: 79.1 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 2
  • Releases: 2
Created about 3 years ago · Last pushed about 2 years ago
Metadata Files
Readme Citation

README.md

Amanita_thiersii and A. foetens

Code and data for A. thiersii/ A. foetens project.

Download genes from NCBI for other saprotrophic Amanitas

Genes: ITS, LSU, SSU, mitochondrial LSU, mitochondrial SSU

Do alignment with MAFFT using the L-INS-i method

  1. Local alignment = L-INS-i algorithm "$ mafft --auto --adjustdirectionaccurately inputfile > outputfile"

After aligning with MAFFT, run IQtree on MAFFT alignments.

  1. "for f in PATH/MAFFTresults/.fasta; do iqtree -s $f -m MFP -msub nuclear -bb 1000 -bnni -pre PATH/iqtree_output/${f##/}; done"

After IQtree, run "cat" to concatenate treefiles.

  1. cat "PATH/iqtree_output/* fasta.treefile > PATH/astral5gene/input5gene.trees"

Then run ASTRAL.

  1. "java -jar ~/Astral/astral.5.7.8.jar -i PATH/astral5gene/input5gene.trees -o PATH/astral5gene/output5geneastral.tre

For details, see file "Code5genetrees.txt"

Owner

  • Name: Nora
  • Login: noramushrooms
  • Kind: user
  • Location: Wisconsin, US

Fungal Biologist

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Dunkirk
    given-names: Nora
    orcid: https://orcid.org/0000-0003-1640-4651
title: noramushrooms/Amanita_thiersii: Data for Amanita thiersii manuscript v1
version: v1.0.0
date-released: 2023-06-01

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