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• Difference between ape::root, ggtree::reroot and phytools::reroot in R
  Hi all, I have been using R to create and manipulate phylogenetic trees for a while, but I was w...
• correlation of genes from two data sets
  Hi I have gene expression data from two different tissues of the same mice/organism. Let say tis...
• Calculate relationship between sequence similarity and scalar distance in a tree
  Hey everyone! I have a 2k multiple sequence alignment tree that I would like to collapse at a cer...
• Phylogenetic tree with 0,1 matrix as the input?
  Hi All, I want to build a tree to reflect the relationship between multiple samples with the fo...
• UBERON. A way to retrieve relationships?
  Dear community, I have gene expression data from several animals, which I'd like to compare. Th...
• Comparing Expression Values From Two Tissues (Under 2 Conditions In 9 Subjects)
  I have a dataset (human microarray) with a total of 36 samples; 9 subjects x 2 conditions x 2 tis...
• Parsing Protein Trees to determine orthologs and paralogs
  Hi Everyone, I'm trying to find orthologs and lineage specific paralogs between two species. I t...
• Clustering and results Display from PART II (PART III) - MeV software version
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• What could be the reasons for Bayesian Inference tree having a different topology from Maximum Likelihood Tree?
  I am trying to look at evolutionary relationships using BI and ML trees. If I have 3 different ev...
• Question regarding Count software
  Hello everybody I read a paper about gene gains and losses between viral genomes, and I want to ...
• how to modify some tiplabs in ggtree?
  Hi there, I am creating a tree with ggtree and the only thing I am not able to do is to modify s...
• How to normalize count data for PCA in R - something goes wrong
  Hi all! I've been trying to do PCA for my RNAseq data to examine the relationship between my samp...
• Best way to visualize large phylogenetic trees
  I am currently creating phylogenetic trees in R to visualize and annotate them. When working with...
• How to scale a cladogram to reflect branching time?
  Hi all, I have a cladogram generated using [PhyloT][1] for 13 yeast species. The tree just show...
• What is the standard way of preparing homolog sequences for a phylogenetic analysis?
  I have two protein sequences with around 50% identity between them. I want to study the phylogen...
• Making Variance Component Analysis Charts in R
  Hello, I am wondering if anyone knows if it is possible to make charts in R similar to the ones ...
• Gene Cluster Phylogenetic Tree
  Hello community :) Question 1. I am comparing the usage of two clustering algorithms, MCL and an...
• Measuring the difference or similarity between two phylogenies
  Hello everyone, I'd like to take two phylogenies for a given nucleotide alignment and create a m...
• How too choose outgroup for rooting a phylogenetic tree?
  I would like to have your opinion about an issue I am dealing with quite often during my work. M...
• Inference orthology relationship
  Extracting orthology relationships follows the main steps of clustering, multiple alignment, and ...