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Questions related to Phylogenetics
HI all-- I'm using ape, and I have a Nexus file with bootstrap support values (eg [&bootstrap=98]). However, when I use R to visualize my tree they don't come through. tree
03 March 2017 5,033 2 View
Does any one know the command string used in paup for CI and RI values? Using Cipres and need to add the command string to get CI and RI values.
01 March 2017 6,724 2 View
I couldn't find good either an online server or standalone tool perform phylogenetic footprinting. I need to perform phylogenetic footprinting across different species. Please do suggest good...
02 February 2017 2,977 1 View
Hello all, I need to get a composite phylogeny for around 80 bat species to perform Phylogenetic Independent Contrasts on some morphological and life history trait data. However, Im an evo scrub...
11 January 2017 6,527 2 View
I am aware that the Consistency Index uses the number of changes in a matrix, but I haven't found a way to do the matrix nor to calculate this index on any software.
02 January 2017 6,930 8 View
"Our study provides insight into how these threats may collectively influence the extinction risk of whole clades, consistent with the supposition that related species, with similar traits, share...
01 January 2017 3,136 0 View
I am interested in determining the phylogenetic relatedness of several species of bacteria distributed throughout a few closely related genera. I have already generated a maximum likelihood...
01 January 2017 3,025 2 View
Hi, I am trying to confirm the bacterial isolates by sequencing. I have targeted lytA gene in Streptococcus pneumoniae. I completed the alignment using CLUSTALW. Now I would like to analyse the...
01 January 2017 6,350 5 View
01 January 2017 655 2 View
01 January 2017 3,157 9 View
I try to run a Beast analysis on 2 genes: cytb and CR. I have run the analysis multiple times, and once the analysis has run, ESS and convergence look good in Tracer. However the output tree is...
29 December 2016 3,228 1 View
Basically, we used RAPD to determine the genetic variation of species from two different populations. In which genetic variation is opposite of genetic similarity. Numerical taxonomy and...
16 December 2016 1,454 3 View
Hi everyone, I want to analysis ITS sequences using Maximum Likelihood (phylogenetic) and UPGMA or Neighbor-Joining (phenetic). I have a situation there. I have been confused to standardized the...
12 December 2016 5,757 3 View
Joel Cracraft listed 7 big questions of systematic biology (ANN. MISSOURI BOT. GARD. 89: 127–144. 2002.). 1. Wat is a species? 2. How many species are there? 3. What is the tree of life? 4. What...
12 December 2016 1,618 0 View
12 December 2016 8,707 5 View
06 December 2016 3,864 3 View
Aim:Are the features that we are interested in more conserved in a set of virus strains than expected? Input:1) 100 virus genomes (strains of same virus) as pairwise aligned sequences (no MSA).2)...
04 December 2016 1,817 5 View
Hybridisation and allopolyploidy can happen between lineages that diverged a long time ago. The 'widest' hybrids that I am aware of are a fern (xCystocarpium roskamianum; Rothfels et al. 2015) and...
20 November 2016 10,040 3 View
11 November 2016 6,034 3 View
I am applying phylogenetic methods for regression to study linear and polynomial correlations between morphological and ecological data. Both my dependent (DEP) and independent (IND) variables are...
10 October 2016 9,593 4 View
Is there a way to restrict ltt.plot to a clade of a large phylogeny created in Beast?
10 October 2016 7,616 2 View
Read 11 answers by scientists to the question asked by Ankush Saddhe on Sep 22, 2016
22 September 2016 3,405 7 View
In morphology, Macrocystidia is supposed to be a close relative genus of Lactocollybia (Singer 1986) as both have gloeocystidia in the context of pileus, stipe, lamellae, etc., but blast searched...
20 September 2016 5,430 8 View
I have thousands influenza sequences and tried so many times. But failed. Is there any detailed demo from the begaining of sequence aligenment to phylogenetic tree building? I hope someone could...
13 September 2016 2,097 3 View