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Questions related to Phylogenetics
Though morphology of the true branched cyanobacteria is indeed tough and there do exist differences of opinions but as I can see, even the phylogenetic information is equally confusing, probably...
08 August 2017 7,805 2 View
I have sequenced a vp1 partial gene of FMD virus and I have detected serotype O with sequence similarity of 95% to the closest on on blast search. I am struggling on how to determine the topotype...
08 August 2017 3,054 3 View
There is a genus I focused, whose phylogenetic histories were obvious different based on chloroplast and nuclear loci. Both topologies were well support. In this case, maybe commonly, how to...
07 July 2017 1,923 4 View
I want to draw a phylogenetics tree using a protein I am working with and its homologs using MEGA7. After the alignment using MUSCLE or CLUSTALW, there are so many options on the MEGA program for...
07 July 2017 5,553 5 View
06 July 2017 4,661 4 View
I am interested in constructing a phylogenetic tree on 30 viruses using their respective DNA polymerase sequences. The problem is that the sequences vary in length and are not as similar as one...
30 June 2017 5,733 2 View
I am currently using R with phangorn and ape to create trees because what I use is binary data. My data is like the one shown in the first figure attached. What I want to get is trees with...
17 June 2017 4,446 2 View
06 June 2017 696 2 View
I’m familiar with strict and majority-rule consensus trees, as well as maximum clade credibility trees, as different ways of summarising results from phylogenetic inference. Recently, I have...
06 June 2017 3,092 0 View
06 June 2017 5,272 3 View
Normally dN/dS ratios are calculated and interpreted as below one negative selection, above 1 is positive selection and 1 means neutral selection. How to interpret dS/dN ratios? Programs like SNAP...
06 June 2017 4,069 9 View
I have been out of the phylogenetics game for a while now (about 3.5 years) but I am needing to update a tree and want to make a good consensus tree. I am building a RAxML, PhyML, IQTree and...
06 June 2017 3,857 2 View
hello, everyone,reciprocal monophyly often treat as a criterion of species delimitation, while it seems no differentiation to monophyly in phylogeny.
16 May 2017 1,545 5 View
We are working on phylogeny of the European Characeae (green algea). We are still missing the following taxa: Nitella capillarisNitella flexilisTolypella intricata Can anyone provide the samples...
05 May 2017 2,230 0 View
Mostly, researchers use phylogenetic turnover calculations to compare phylogenies among communities, test hypothesis relied on enviromental heterogeneity (e.g. climate) among communities, biomes...
05 May 2017 3,067 0 View
05 May 2017 9,233 6 View
I was wondering what people’s thoughts on this topic were: how many SNPs per RAD locus should be used for phylogenetic studies? All agree this is important, with fewer SNPs per locus being...
04 April 2017 8,269 4 View
phylogentic tree, MEGA6
04 April 2017 4,685 8 View
I'm working on testing some trait correlations and am wanting to use phylogenetic correction (since the species I've gotten the data from are closely related). It's not a particularly complex...
04 April 2017 829 1 View
There are some examples given in PopArt manual. Below is the geotags table. seq_2 54.756365N 20.559500E 10seq_2 43.362073N 85.087465E 5seq_2 27.743932N 134.852156E 6seq_7 6.903639N 28.416291E...
04 April 2017 2,270 4 View
Constructing phylogenetic trees in BEAST package and MrBayes requires an AIC selected best-fit substitution model. Running a model search in mrmodeltest requires a script created in PAUP.
29 March 2017 6,901 4 View
There is a commentary in Langille et al., 2013: Predictive functional profiling of microbial communities using 16S r RNA marker gene sequences. "More sequencing is needed to profile functional...
28 March 2017 7,191 3 View
03 March 2017 2,346 6 View
03 March 2017 5,035 3 View