Resources

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Bioinformatics tutorials (written by Jacob L. Steenwyk)

Phylogenetics/Phylogenomics
  • Five-step phylogenomics
  • Inferring a phylogeny, from sequences to tree
  • Trim multiple sequence alignments
  • Evaluate the accuracy of a multiple sequence alignment
  • Calculate gene-gene covariation
  • Summarize information content in phylogenomic data
  • Identifying signatures of rapid radiation
  • Prune phylogenies using a GUI
    • UNIX challenges
  • Math and string replacements - Beginner
  • Looping through multiple gff files - Beginner
  • If statements - Beginner
    • Making figures in R (Beginner)
  • Presentation
  • Worksheet
  • Answer sheet

    • Other Science-related Resources

    Coding
  • UNIX Tutorial for Beginners
  • An introduction to R
  • Unix and perl oneliners for Bioinformatics
    • Statistics
  • Statistical thinking and analysis
  • Enrichment analysis
  • Multiple linear regression analysis in R
  • Kruskal-Wallis & post-hoc tests
    • Phylogenetics
  • Alignment format conversion
  • CIPRES Science Gateway
  • Estimating diversification rates
  • Introduction to Phylogenetic Biology
    • Genomics
  • The basics of SAMTools
  • Using CNVnator
  • R package for detecting recombination
  • Reciprocal best BLAST hit
    • Figure making
  • Top 50 ggplot2 Visualizations
  • Visualize correlations
  • PCA/clustering visualization
  • Colortools for large color palettes
    • ACCRE
  • Lmod - loading modules
  • Example job array
  • Using Python on ACCRE
    • Sequence Similarity Searches
  • Identify homologs using HMMs
  • Construct a BLAST database
  • Basic HMMER usage

    • Mental Health

    Crisis Resources
  • National Suicide Prevention Lifeline: 1-800-273-TALK (8255)
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  • National Domestic Violence Hotline: 1-800-799-SAFE (7233)
  • Lesbian, Gay, Bisexual and Transgender National Hotline: 1-888-843-4564
    • Therapy
  • American Psychological Association
  • Psychology Today
  • Talkspace
  • BetterHelp