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--- phylogenetic_analysis_for_dummies [2017/11/14 13:09] – hyjeong
+++ phylogenetic_analysis_for_dummies [2022/05/02 08:21] (current) – [Figtree] hyjeong
@@ Line 1: / Line 1: @@
 ====== Phylogenetic analysis for dummies ======
-http://epidemic.bio.ed.ac.uk/how_to_read_a_phylogeny
+  * 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
-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]]
-A tutorial: https://home.ccr.cancer.gov/lco/DrawingTrees.htm
+  * [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 ====
@@ Line 24: / Line 28: @@
 ===== 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."
+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/
+  * 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/