Genome Informatics Laboratory at KRIBB

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====== Phylogenetic analysis for dummies ======
  * http://epidemic.bio.ed.ac.uk/how_to_read_a_phylogeny
  * Phylogeny.fr: Robust Phylogenetic Analysis for the non-specialist http://phylogeny.lirmm.fr/phylo_cgi/index.cgi
  * A tutorial: https://home.ccr.cancer.gov/lco/DrawingTrees.htm
  * [John Innes Centre] [[http://training.scicomp.jic.ac.uk/docs/phylogenetics_course_book/index.html|Introduction to Phylogenetics]]
  * [ResearchGate] [[https://www.researchgate.net/post/How_can_I_interpret_bootstrap_values_on_phylogenetic_trees_built_with_Maximum_Likelihood_method|How can I interpret bootstrap values on phylogenetic trees built with Maximum Likelihood method?]]
  * [[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116784/|A practical guide to phylogenetics for nonexperts]]
  * [NCBI Bookshelf] [[https://www.ncbi.nlm.nih.gov/books/NBK21122/|Chapter 16. Molecular phylogenetics]]
===== Sequence manipulaton =====
  * trimAl: a tool for automated alignment trimming in large-scale phylogenetic analysis
  * [[https://github.com/PatrickKueck/FASconCAT|FASconCAT]]: convenient handling of large data matrices
===== All-in-one =====
==== MEGA ====
http://www.megasoftware.net/

==== MAFFT server ====

http://mafft.cbrc.jp/alignment/server/ [[http://www.incodom.kr/MAFFT|인코돔에 소개된 MAFFT]]

웹 브라우저에서 파일을 전송하면 다음과 같이 화면이 바뀐다. 

{{ :mafft.png?600 |}}

웹 브라우저 내에서 결과를 시각적으로 표현하는 다양한 기능이 내장되어 있어서 대단히 유용하다(감동적이다!). 서열정렬 결과의 시각화에는 [[https://www.ncbi.nlm.nih.gov/pubmed/27412096}MSAViewer]] 및, [[https://academic.oup.com/bioinformatics/article/25/9/1189/203460/Jalview-Version-2-a-multiple-sequence-alignment|Jalview]], NJ(<2,000 sequences) or UPGMA 트리 시각화에는 [[https://arxiv.org/abs/1602.04258|Phylo.io]]가 쓰인다. 물론 다른 선택도 가능하다.

프로그램 일반 사항(version 7) http://mafft.cbrc.jp/alignment/software/

===== Tree visualization =====
==== Figtree ====
http://tree.bio.ed.ac.uk/software/figtree/ "FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, **it was written for my own needs so may not be as polished and feature-complete as a commercial program**. In particular it is designed to display summarized and annotated trees produced by BEAST." 
==== Archaeopteryx ====
https://sites.google.com/site/cmzmasek/home/software/archaeopteryx A software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. Archaeopteryx is entirely written in the Java programming language. It can be used both as a standalone application and an applet.[omicstools]

==== Online tool ====
  * Phylogenetic tree (newick) viewer http://etetoolkit.org/treeview/
  * EvolView: an online phylogenetic tree viewer and customization tool http://www.evolgenius.info/evolview/
  * iTOL (Interactive Tree Of Life) https://itol.embl.de/

==== Tree visualization with data ====
  * https://holtlab.net/2015/10/03/plotting-trees-data/
  * https://github.com/katholt/plotTree
  * http://borensteinlab.com/courses/GS_373_12_sp/slides/W9C2-DistTrees.pdf
  * GraPhlAn https://peerj.com/articles/1029/



===== 다른 자료 =====
  * [[http://www.jcsantosresearch.org/Class_2014_Spring_Comparative/pdf/week_6/Feb_12_2015_Chronograms.pdf|Manipulate trees using FigTree and R]]
  * Rooting Trees, Methods for https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149615/