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Finishing up Final Project from Andrew Verdegaal #9

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Finishing up Final Project from Andrew Verdegaal #9

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Commits on Feb 14, 2019

  1. Adding goal to final project (Salmonella)

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    aaverdegaal committed Feb 14, 2019
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Commits on Feb 19, 2019

  1. Added intro and goals to readme

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    aaverdegaal committed Feb 19, 2019
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  2. Added papers relevant to project

    @aaverdegaal
    aaverdegaal committed Feb 19, 2019
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  3. Added extensive info on data/ methods to be used in course of project… 

    …; background added for project
    @aaverdegaal
    aaverdegaal committed Feb 19, 2019
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  4. Attempted to fix format of methods

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    aaverdegaal committed Feb 19, 2019
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Commits on Mar 7, 2019

  1. Added database sources, including links; altered goals, alternate goa… 

    …l added
    @aaverdegaal
    aaverdegaal committed Mar 7, 2019
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  2. Attempted to fix some formatting issues; getting hang of how to forma… 

    …t on GitHub
    @aaverdegaal
    aaverdegaal committed Mar 7, 2019
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Commits on Mar 8, 2019

  1. Added some new data sources; new tools

    @aaverdegaal
    aaverdegaal committed Mar 8, 2019
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  2. Messing with formatting

    @aaverdegaal
    aaverdegaal committed Mar 8, 2019
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  3. Added/changed some information in the goals section; Reformatted it a… 

    …s well
    @aaverdegaal
    aaverdegaal committed Mar 8, 2019
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  4. Added more tools; added a new approach that I may take

    @aaverdegaal
    aaverdegaal committed Mar 8, 2019
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Commits on Apr 4, 2019

  1. Added what to look at in methods

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    aaverdegaal committed Apr 4, 2019
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  2. New method for phylogenetic analysis; paper with it

    @aaverdegaal
    aaverdegaal committed Apr 4, 2019
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Commits on Apr 5, 2019

  1. Changed specific goals and big picture (focusing on gene loss phyloge… 

    …netic relationships)
    @aaverdegaal
    aaverdegaal committed Apr 5, 2019
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  2. Added script used to annotate specific Salmonella genomes, aiming at … 

    …a uniformed file mix to use for initial phylogenetic analysis/ genome comparison
    @aaverdegaal
    aaverdegaal committed Apr 5, 2019
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  3. Added new phylogenetic software tool

    @aaverdegaal
    aaverdegaal committed Apr 5, 2019
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  4. Beginning to work on analysis

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    aaverdegaal committed Apr 5, 2019
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Commits on Apr 8, 2019

  1. Been working on analyzing six Salmonella genomes using ClustAGE pipel… 

    …ine; added notes on work and images produced thus far
    @aaverdegaal
    aaverdegaal committed Apr 8, 2019
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Commits on Apr 9, 2019

  1. Re-did ClustAGE analysis using my own computer; Added plots made from… 

    … this analysis, including individual graphs of dissimilar accessory regions; added more notes
    @aaverdegaal
    aaverdegaal committed Apr 9, 2019
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  2. Added more notes on process I am currently working on, mainly trying … 

    …to find alternative methods to align Salmonella genomes and then construct a phylogenetic tree through FastTree or Phylip
    @aaverdegaal
    aaverdegaal committed Apr 9, 2019
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Commits on Apr 10, 2019

  1. Added more notes; working on best alignment method still and which do… 

    …wnstream programs to use; this project may turn into comparing alignment/ phylogenetic methods for bacterial whole genome study
    @aaverdegaal
    aaverdegaal committed Apr 10, 2019
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Commits on Apr 15, 2019

  1. Working on alignment again, got data from CSI_Phylo pipeline; added n… 

    …otes about today and some papers
    @aaverdegaal
    aaverdegaal committed Apr 15, 2019
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  2. Added more notes, working on ClustAGE and ClustalFrameML pipelines

    @aaverdegaal
    aaverdegaal committed Apr 15, 2019
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Commits on Apr 16, 2019

  1. Revamped readme.md, changing scope of project and honing in on an ana… 

    …lysis pipeline; Added a couple papers and notes for today and yesterday
    @aaverdegaal
    aaverdegaal committed Apr 16, 2019
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  2. Changed some readme.md format; Added to obstacles and what would have… 

    … done different
    @aaverdegaal
    aaverdegaal committed Apr 16, 2019
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  3. fixed formatting in notes

    @aaverdegaal
    aaverdegaal committed Apr 16, 2019
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  4. Removed papers, added plots/ some data from ClustAGE pipeline

    @aaverdegaal
    aaverdegaal committed Apr 16, 2019
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  5. Fixed some typos in readme.md; Changed goals and their wording

    @aaverdegaal
    aaverdegaal committed Apr 16, 2019
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  6. Fixed some typos and formatting in project notes

    @aaverdegaal
    aaverdegaal committed Apr 16, 2019
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Commits on Apr 18, 2019

  1. Added project notes, plan; Added accession list of chromosomes/ plasm… 

    …ids used as references in analysis
    @aaverdegaal
    aaverdegaal committed Apr 18, 2019
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  2. More notes; testing markdown of readme sequence names

    @aaverdegaal
    aaverdegaal committed Apr 18, 2019
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  3. More formatting

    @aaverdegaal
    aaverdegaal committed Apr 18, 2019
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  4. More formatting for sequences

    @aaverdegaal
    aaverdegaal committed Apr 18, 2019
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  5. Multiple directory changes; added notes; papers

    @aaverdegaal
    aaverdegaal committed Apr 18, 2019
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Commits on Apr 19, 2019

  1. Added citations; notes; ClustAGE specific findings; tools

    @aaverdegaal
    aaverdegaal committed Apr 19, 2019
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  2. Added ppt file; Added data, images for presentation; Notes/citations

    @aaverdegaal
    aaverdegaal committed Apr 19, 2019
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  3. Citations added; Ppt updated; More data added

    @aaverdegaal
    aaverdegaal committed Apr 19, 2019
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Commits on Apr 20, 2019

  1. Added to ppt; Citations

    @aaverdegaal
    aaverdegaal committed Apr 20, 2019
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  2. Added to ppt done?

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    aaverdegaal committed Apr 20, 2019
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Commits on Apr 21, 2019

  1. Updated ppt; Updated Readme file (citations, methods, results, data, … 

    …issues)
    @aaverdegaal
    aaverdegaal committed Apr 21, 2019
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  2. Updated ppt; Updated Readme file (citations, methods, results, data, … 

    …issues)
    @aaverdegaal
    aaverdegaal committed Apr 21, 2019
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  3. Added to readme

    @aaverdegaal
    aaverdegaal committed Apr 21, 2019
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  4. Fixed some ppt; Added to readme (methods, citations)

    @aaverdegaal
    aaverdegaal committed Apr 21, 2019
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  5. Fixed some ppt; Added to readme (methods, citations)

    @aaverdegaal
    aaverdegaal committed Apr 21, 2019
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Commits on Apr 25, 2019

  1. Any changes not included

    @aaverdegaal
    aaverdegaal committed Apr 25, 2019
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  2. Testing adding code to Project Notes md file

    @aaverdegaal
    aaverdegaal committed Apr 25, 2019
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  3. Testing again

    @aaverdegaal
    aaverdegaal committed Apr 25, 2019
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  4. Edited and formatted the Project_notes.md for better viewing and clarity

    @aaverdegaal
    aaverdegaal committed Apr 25, 2019
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  5. Reshuffled data, added relevant data sets for annotation, assembly, s… 

    …pine, agent, and Clustage pipeline; modified and added notes that were missing
    @aaverdegaal
    aaverdegaal committed Apr 25, 2019
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  6. Fixed spine file, removed

    @aaverdegaal
    aaverdegaal committed Apr 25, 2019
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  7. Added more notes; Added citations; Fixed citations

    @aaverdegaal
    aaverdegaal committed Apr 25, 2019
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