Note

A paper a day

A Paper A Day May Week 1 0% 07 [[Zimpel 2020 Global Distribution Evolution|Zimpel et al (2020)...

Auspice

Auspice Summary Auspice is software that performs visualization of [[Phylogenetic phylogenies]]. Configu...

Bayesian evaluation of temporal signal

Bayesian Evaluation of Temporal Signal

Bioinformatics pipeline

Bioinformatics Pipeline Literature [[Snakemake]] [[nf-core/eager]]

Bison Mitochondria

Bison Mitochondria [[Bison Mitochondria]] started out as a single notes (like the others) but grew into its own folder of concepts. Peo...

Bootstrapping an existing tree

Bootstrapping an Existing Tree LSD Tree iqtree \ -s lsd.filter.aln \ -te lsd.filter.nwk \ -m K3Pu+F+I \ -b 10 \ -pre test \ ...

Coefficient of variation

Coefficient of Variation Standard deviation of branch lengths divided by mean branch length.

Curate

Curate

Eroshenko et al. 2021 evolution circulation yersinia

Eroshenko et al. 2021 Evolution Circulation Yersinia Field Value Title [[Evolution]] an...

Extract pages from a pdf

Extract Pages from a PDF gs -sDEVICE=pdfwrite -dNOPAUSE -dBATCH -dFirstPage=2 -dLastPage=3 -sOutputFile=output.pdf input.pdf

Figtree

Figtree Summary Figtree is software that performs visualization of phylogenetic trees. Command-Line figtree -graphic PDF test.nwk tes...

Footnote Shortcut

Footnote Shortcut Summary Footnote Shortcut that adds footnotes. Functions After installing and activating this plugin, you still hav...

Geocode

Geocode Literature [[GeoPy]] [[Nominatim]] [[OpenStreetMap]]

ImageMagick

ImageMagick Summary ImageMagick is software that converts image formats. Security Several formats requiring changing ImageMagick's se...

Integrated writing

Integrated Writing I have multiple different platforms that I write in. I would like to [[Integrated Writing Integr...

Isolation by distance

Isolation By Distance

Mvp

MVP [[MVP]] is a [[CSS]], shown at https://andybrewer.github.io/mvp/. [[@vimalkvn]] has a [[pandoc]] compatible version at https://gitla...

Makeover monday

Makeover Monday [Makeover Monday A weekly social data project](https://www.makeovermonday.co.uk/)

Mcmaster thesis pandoc template

McMaster Thesis Pandoc Template Setup [[McMaster]] Thesis Template Download the [[LaTeX]] thesis template from http://www.cas.mcmas...

Metadata

Metadata

NCBImeta

NCBImeta Summary [[NCBImeta]] is a command-line application that retrieves and organizes metadata from the [[National Ce...

National centre for biotechnology information

National Centre for Biotechnology Information

Nextstrain citations

Nextstrain Citations I want to be able to add and manage citations in [[Nextstrain]] and [[Auspice]]. I want to write [[Nextstrain ...

Nokogiri

Nokogiri Summary Nokogiri is a [[Ruby]] module for working with [[XML]] and [[HTML]]. Whenever I try to build [[Jekyll]] sites, I almo...

Obsidian Citations

Obsidian Citations Summary Obsidian Citations is a plugin that integrates citations with [[Zotero]]. Now open the Obsidian preferences...

Obsidian

Obsidian Tasks Pending table tags from "" where project=[[Obsidian]] and status!="done" Completed table tags from "" where project=...

PhD Dissertation

PhD Dissertation Projects [[NCBImeta]] [[Plague Phylodynamics and Phylogeography]] [[Plague Denmark]] Graph Filters: [[Projec...

Plague Genome Curation

Plague Genome Curation Literature Review [[Bioinformatics Pipeline]] [[Geocode]]

Plague Phylodynamics and Phylogeography

Plague Phylodynamics and Phylogeography Experiments [[Plague Genome Curation]] [[Plague Phylodynamics]] [[Plague Phylogeography]...

Rasmussen et al. 2015 early divergent strains

Rasmussen et al. 2015 Early Divergent Strains Field Value Title Early divergent strains...

Sagulenko et al. 2018 treetime maximum Likelihood phylodynamic

Sagulenko et al. 2018 TreeTime Maximum-Likelihood Phylodynamic Field Value Title [[Tree...

Sed Fix Tree Files

Sed Fix Tree Files Tasks task from "tasks" where contains(file.name, "Sed Fix Tree Files") Code 100.00:20.70040[\[&date="-139.09...

Shortcuts Extender

Shortcuts Extender Summary Shortcuts Extender adds additional shortcuts to [[Obsidian]]. Functions Changing the Heading Level To c...

Snakemake

Snakemake Summary Snakemake is software that performs… tags: [[Tool]], #📝/🌱

Spyrou et al. 2018 analysis 3800 Year Old yersinia

Spyrou et al. 2018 Analysis 3800-Year-Old Yersinia Field Value Title Analysis of 3800-y...

Tidy Footnotes

Tidy Footnotes Summary Tidy Footnotes is a plugin that organizes footnotes. Functions Adds the command Tidy Footnotes. Whoops, here'...

Wagner et al. 2014 yersinia pestis plague

Wagner et al. 2014 Yersinia Pestis Plague Field Value Title Yersinia pestis and the Pla...

Xu et al. 2019 historical genomic data

Xu et al. 2019 Historical Genomic Data Field Value Title Historical and genomic data re...

Yersinia pestis

[[Yersinia pestis]] Phylogenetic Branches [[Branch]] [[Clade]] Subclade [[Branch 0]] ...

1000 Plagues in the Genomics Age

{}

{{title}} Summary {{title}} is software that performs…

wkhtmltopdf

wkhtmltopdf Configure [[Ubuntu]] ```bash sudo vi /etc/apt/sources.list #add following line at the end of file deb http://security.u...

wkhtmltopdf

wkhtmltopdf Configure Ubuntu ```bash sudo vi /etc/apt/sources.list #add following line at the end of file deb http://security.ubunt...