User: DNAngel

gravatar for DNAngel
DNAngel30
Reputation:
30
Status:
New User
Location:
Last seen:
7 hours ago
Joined:
2 years, 4 months ago
Email:
k********************@hotmail.com

Posts by DNAngel

<prev • 51 results • page 1 of 6 • next >
0
votes
0
answers
53
views
0
answers
How to test evolutionary rates for each species in a gene alignment?
... I was wondering if there are any R packages or tools that can determine the evolutionary rates of species given their tree (with branch lengths) and an alignment file for a specific gene. I want to see if some species belonging to a clade are evolving more quickly than the ancestral clades. Is this ...
R evolutionary rate written 12 days ago by DNAngel30
0
votes
0
answers
96
views
0
answers
R package to calculate ancestral state characters using maximum parsimony?
... Hello, I was wondering if anyone knew of a program or R package that calculates ancestral character states of discrete traits (i.e. habitat, skin colour) using maximum parsimony? The ape package utilizes models that are all likelihood based. I want to implement both methods and compare the results ...
R ancestral states maximum parsimony written 3 months ago by DNAngel30
0
votes
0
answers
161
views
0
answers
Is there a tool to calculate sequence similarity of sequences in a MSA?
... I have many multiple sequence alignments containing protein-coding genes aligned by codons and I want to generate pairwise similarity tables between each pair of sequences. I know Geneious used to do this but I no longer have it on trial nor can I afford to buy it. ...
alignment dna written 3 months ago by DNAngel30
0
votes
0
answers
151
views
0
answers
Theory question on dN/dS values for phylogeny
... Hi all, This might be a noob question but I was just wondering, what does it mean if an internal branch has a higher dN/dS ratio but the tips leading from that branch have low dN/dS values. I ran the M0 model for a gene just to test things and understand the output data. Here's an example of what ...
dnds codeml paml written 4 months ago by DNAngel30
0
votes
1
answer
255
views
1
answers
Comment: C: Help with understanding PAML M0 output
... Okay I can try the free ratio model as well, but I don't think it gives me individual dN and dS values with their individual branch lengths. I have to make a dN and dS tree where I can use their individual branch lengths and compare the differences visually in that manner. M0 gives individual dN and ...
written 4 months ago by DNAngel30
0
votes
1
answer
255
views
1
answers
Comment: C: Help with understanding PAML M0 output
... Also, why would model M1a be used to check for branch-specific dN and dS? Why not model M0 which doesn't constrain it since M1a does not allow positive selection anyways? ...
written 4 months ago by DNAngel30
0
votes
1
answer
255
views
1
answers
Comment: C: Help with understanding PAML M0 output
... I am confused still, if there are 2000 N and only 650 S, how is the overall dN/dS less than 1? ...
written 4 months ago by DNAngel30
0
votes
1
answer
255
views
1
answer
Help with understanding PAML M0 output
... Hi all, Could someone just clarify the following output for me? Example output: branch t N S dN/dS dN dS N*dN S*dS 38..1 0.431 2257.5 655.5 0.0546 0.0294 0.5379 66.3 352.6 38..39 0.068 2257.5 655.5 0.0546 0.0046 0.0843 10. ...
paml m0 written 4 months ago by DNAngel30 • updated 4 months ago by Dave Carlson90
5
votes
2
answers
288
views
5 follow
2
answers
Does Whole Exome Sequencing Include Mitochondrial Genome??
... I have exome sequencing data and as far as I know, it should include all exonic regions including the mitochondrial genome. When I blast my sequences to recover mitochondrial protein-coding genes, I get a ton of intermittent stop codons and a lot of gaps which I generally do not find when extracting ...
exome mitogenome whole exome sequencing written 4 months ago by DNAngel30 • updated 4 months ago by Jeremy Leipzig18k
0
votes
0
answers
184
views
0
answers
Comment: C: How to set up a reference file for BWA so that highly variable sites between con
... How would I use Blast+ if my organisms don't have references or have the genes sequenced previously?? The reference species exists on ensembl so would that be an option? I do have a lot of reads, each species has over 1 million single-end reads. ...
written 5 months ago by DNAngel30

Latest awards to DNAngel

Scholar 8 months ago, created an answer that has been accepted. For A: How to save trimmomatic terminal summary to an output file?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 836 users visited in the last hour