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Finishing up Final Project from Andrew Verdegaal #9
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Commits on Feb 14, 2019
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Commits on Feb 19, 2019
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Added extensive info on data/ methods to be used in course of project…
…; background added for project
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Commits on Mar 7, 2019
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Commits on Mar 8, 2019
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Commits on Apr 4, 2019
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Commits on Apr 5, 2019
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Changed specific goals and big picture (focusing on gene loss phyloge…
…netic relationships)
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Added script used to annotate specific Salmonella genomes, aiming at …
…a uniformed file mix to use for initial phylogenetic analysis/ genome comparison
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Commits on Apr 8, 2019
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Been working on analyzing six Salmonella genomes using ClustAGE pipel…
…ine; added notes on work and images produced thus far
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Commits on Apr 9, 2019
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Re-did ClustAGE analysis using my own computer; Added plots made from…
… this analysis, including individual graphs of dissimilar accessory regions; added more notes
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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
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Commits on Apr 10, 2019
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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
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Commits on Apr 15, 2019
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Working on alignment again, got data from CSI_Phylo pipeline; added n…
…otes about today and some papers
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Commits on Apr 16, 2019
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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
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Commits on Apr 18, 2019
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Added project notes, plan; Added accession list of chromosomes/ plasm…
…ids used as references in analysis
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Commits on Apr 19, 2019
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Commits on Apr 20, 2019
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Commits on Apr 21, 2019
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Commits on Apr 25, 2019
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Reshuffled data, added relevant data sets for annotation, assembly, s…
…pine, agent, and Clustage pipeline; modified and added notes that were missing
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