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Questions related to Phylogenetics
I am using MEGA to build a phylogenetic tree using two genes. They were already aligned separatelly using MUSCLE, but now I don't know how to continue...
06 June 2016 6,530 7 View
I finally got a decent-looking tree using back-translated protein sequences to align the nucleotides of bacterial genome regions that span (12-20)kb. I used NJ algorithm and Jukes-Cantor...
06 June 2016 1,602 3 View
I have constructed phylogenetic trees of mites using 16s rRNA and 18s rRna. I've got 4 sequences for one gene, out of which one is showing similarity with the outgroup . What can be the possible...
06 June 2016 3,512 3 View
Hello, Does anybody know what phylogenetic reconstruction method is best suited to build a tree with palindromic sequences from several lines of the same Drosophila species? I'm trying to sequence...
06 June 2016 4,914 2 View
Thinking in phylogenetic inference, I have two questions: 1) How I can proceed when I have two different rates of nucleotide substitution in my data? and 2) How to know if two mitochondrial...
06 June 2016 2,941 0 View
I have reconstructed the phylogenetic relationship of a kind of mammal using different mtDNA and generated different results. Specially, four consistent clades were resolved by different mtDNA,...
06 June 2016 2,017 7 View
How do I translate phylogenetic tree-Neighbor joining to explain the related species to my identified isolate. Because my sequencing results indicated 99% relation with my isolate and other...
20 May 2016 1,812 3 View
Is there any kind of software/program can test bi-branch or multi-branch phylogensis of the speciation?
15 May 2016 5,253 3 View
I did the ancestral states reconstruction in Mesquite v. 3.04, and the character has 3 states. I use 0&1 or 0&2 to indicate this species has polymorphic states, then I analyzed my data...
05 May 2016 7,445 6 View
I am working to characterize very specific region between two bacterial species that spans from 13kb to 20kb in size, and each contains from 8 to 13 genes. I plan to use the protein sequences to...
05 May 2016 2,069 9 View
05 May 2016 7,985 4 View
05 May 2016 770 3 View
Is there any software (desktop or online) that allows you to create customizable visualizations of the most current phylogenetic relationships between taxons? Let's say that I would like to have...
28 April 2016 770 6 View
I want to start this thread to discuss some possible ways to simultaneously quantify multiple (20+) microorganisms (phylogenetically unrelated). qPCR or ddPCR basically can only target one or a...
15 April 2016 5,201 3 View
I want to look for galactose-alpha-1,3-galactose in ticks and for the presence of mammalian blood at the same time. I only found primers for vertebrates or species specific ones. But i only need...
04 April 2016 1,375 5 View
I am doing a study on phylogeography. An average pairwise difference and Nei's distance matrix was generated in Arlequin. I am having a hard time interpreting the results. As far as I know, higher...
04 April 2016 6,710 2 View
Plant mitochondrial pseudogenes tend to accumulate neutral mutations useful for phylogenetic/genetic diversity studies. However, they could be duplicated in nuclear genome in some species. With...
04 April 2016 6,715 16 View
According to Mayfield and Levine (2010), when two competing species differ primarily in their niches, competition causes trait overdispersion (divergence), but when they differ primarily in their...
04 April 2016 3,413 4 View
04 April 2016 2,433 4 View
Dear, I have a community data matrix (presence and absence) and a phylogenetic tree created by ape package in R. But when I try calculate correlation between co-occurrence of species and its...
04 April 2016 2,733 1 View
Maximum-likelihood (ML) tree based on GTR, why we choose this GTR mode to construct a phylogenetic tree? Could anybody explain it with ref/article if there is any? I may find answer in Nei and...
04 April 2016 8,394 10 View
Cryptosporidium parvum ,phylogenetic
04 April 2016 6,893 2 View
I want to concatenate multiple protein coding gene (PCGs) sequences of an organism and calculate base composition at each codon position of concatenated PCGs in MEGA 6.0. Which software/ tool can...
04 April 2016 7,167 3 View
04 April 2016 9,908 7 View