User: anuragm

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anuragm130
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Posts by anuragm

<prev • 45 results • page 1 of 5 • next >
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GTR always the best model of evolution
... Hi I was studying models for constructing phylogenetic trees. It is mentioned that all other models are 'nested' within GTR model i.e. can be arrived upon by constraining some parameters in GTR. Why should we do a model test at all and instead use a GTR model every single time because as I understa ...
gtr nucleotide evolution models phylogenetics written 4.7 years ago by anuragm130 • updated 4.7 years ago by Brice Sarver3.3k
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What sample sizes and degree of polymorphism within the samples are ideal for carrying out Bayesian Skyline Plots?
... I am interested in creating Bayesian Skyline Plots to look at demographic changes in certain population groups. However, these populations have very little within population variation. Around 5 polymorphic sites within each population and one dominating haplotype that comprises almost 90% of the pop ...
demography beast population genetics written 4.9 years ago by anuragm130
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Intuitive explanation for Fu's Fs statistic
... I am trying to grasp what Fu's Fs intuitively means. Kent Holsinger's Population genetics notes states "S is the probability of observing a random sample with a number of alleles equal to or smaller than the observed value under given the observed level of diversity and the assumption that all of t ...
statistic selection population genetics written 4.9 years ago by anuragm130 • updated 4.7 years ago by Biostar ♦♦ 20
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Comment: C: What could be the reasons for Bayesian Inference tree having a different topolog
... Yes, using GTR in both   ...
written 4.9 years ago by anuragm130
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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 evolutionary lineages BI gives a node between lineages 1 and 2 (1 and 2 diverged from a common ancestor) whereas ML gives a node between lineages 2 and 3 (2 and 3 diverged from a common ancestor). What cou ...
phylogeny bayesian maximum likelihood written 4.9 years ago by anuragm130 • updated 4.9 years ago by 5heikki8.6k
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Divergence time estimates using BEAST
... I am interested in using BEAST to find the divergence time estimates of species separations within a genus of frogs. The genus separated from a outgroup taxon I have chosen around 80 million years ago. Thats all the information I have. Is it possible for me to do a divergence analysis using BEAST an ...
beast divergence written 4.9 years ago by anuragm130 • updated 4.9 years ago by Brice Sarver3.3k
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How does Bayesian Skyline plot estimate population size changes through time ?
... I am new to analysing demography using Bayesian Skyline plots. I was wondering how using parameters could estimate population sizes through generations from a sequence alignment of DNA sequences from a population ?   Suppose a population has 5 haplotypes, with one particular haplotype in excess ma ...
demography bayesian population genetics written 4.9 years ago by anuragm130
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Comment: C: Why 4Ne Rather Than 2Ne?
... "expected time for coalescence of 2 alleles from a diploid population undergoing a neutral evolution is 2N{e}" - Could you please explain how ? I am sorry I could not fully grasp that part. ...
written 4.9 years ago by anuragm130
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Ancestral Sequence Reconstruction from Multiple Sequence Alignment using Mesquite
... I have a nexus tree file and a multiple sequence alignment(MSA) in nexus format. I am interested in ancestral sequence reconstruction using Mesquite. I had been following this tutorial : http://phylo.bio.ku.edu/slides/lab9-MesquiteAncStatesBisse/09-Mesquite.html#Part_B:_Estimating_ancestral_states   ...
mesquite ancestral state written 4.9 years ago by anuragm130 • updated 4.9 years ago by rmccloskey210
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Comment: C: Infer ancestral sequence from a Multiple Sequence Alignment
... FastML crashed multiple times, just like it is mentioned! ...
written 5.0 years ago by anuragm130

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Popular Question 4.9 years ago, created a question with more than 1,000 views. For Calculating Phastcons And Phylop Scores

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