User: al-ash

gravatar for al-ash
al-ash100
Reputation:
100
Status:
Trusted
Location:
Japan/Okinawa/OIST
Last seen:
2 weeks, 2 days ago
Joined:
4 years, 1 month ago
Email:
b*********@gmail.com

Posts by al-ash

<prev • 66 results • page 1 of 7 • next >
0
votes
10
answers
43k
views
10
answers
Comment: C: Multiline Fasta To Single Line Fasta
... ...the link is dead and I still get the first line empty after redirecting the output into a file - could you update the answer if there is a more elegant way (not piping through tail) to avoid this? ...
written 3 months ago by al-ash100
0
votes
0
answers
1.0k
views
0
answers
Comment: A: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
... "ITS (Internal Transcribed Spacer) is part of the non-transcriptional region of the fungal rRNA gene" is a bit misleading (it is like defining DNA as the genetic information carrier of birds - i.e. not incorrect, but...) ...
written 4 months ago by al-ash100
0
votes
4
answers
3.4k
views
4
answers
Comment: C: SRX from SRR IDs
... Be careful though when converting larger number of accessions. When converting ca 500 Sample accessions to Run accessions, somewhere in the middle of the process, one conversion failed for me with "Can't fetch uids from history because of: Result not ready". ...
written 4 months ago by al-ash100
0
votes
0
answers
265
views
0
answers
Comment: C: Generate all bifurkating newick trees given for N taxa
... Thanks! https://stackoverflow.com/questions/46626414/how-do-i-generate-all-possible-newick-tree-permutations-for-a-set-of-species-giv/46670077#46670077 is very close - I think I can generate the bifurcating trees by taking this solution and removing the polytomies (which I can do here by e.g. removi ...
written 6 months ago by al-ash100
0
votes
0
answers
265
views
0
answers
Generate all possible bifurkating newick trees for N taxa
... I'd like to generate all existing bifurkating newick trees for a set of N taxa (specifically N=5 for my task but I would prefer a general solution for N). The tool or code would ideally take as input a set of N strings (e.g. "species1","species2","species3","species4","species5") and generate all p ...
generate tree newick written 6 months ago by al-ash100
0
votes
0
answers
363
views
0
answers
Comment: C: Combine node/branch labels from multiple trees into one
... I think consensus() is not doing what I'm looking for here - to compare a reference tree with a set of some other trees and generate a tree with the same topology as the reference tree but additionally containing conflict/support information accumulated from all the other input trees. ...
written 6 months ago by al-ash100
0
votes
0
answers
363
views
0
answers
Combine node/branch labels from multiple trees into one
... I'd like to combine boostraps/priors from multiple phylogenetic trees onto a reference tree topology. The trees would contain identical set of taxa (tip labels) and distinct node/branch values. In the resulting tree, the node/branch information from the trees should be saved into the reference tree ...
annotation label tree treegraph2 written 6 months ago by al-ash100
0
votes
2
answers
1.1k
views
2
answers
Answer: A: yn00 in PAML returns error: Error in sequence data file: E at 3 seq 1.
... Please show also the headers of the alignments which "are fine" to see if the problem is header length. I had this error when my input phylip file had between sequence name and sequence tab instead of two spaces. Replacing the tab by two spaces (e.g. in bash via sed 's/\t/ /') fixed the problem - ...
written 6 months ago by al-ash100
1
vote
2
answers
3.2k
views
2
answers
Answer: A: Manual edit of multiple alignment
... Since this is one of the top hits when searching online for manual editing of multiple alignments, I'd like to reopen this topic to hopefully collect suggestions for some more tools than JalView for visual inspection and editing of multiple sequence alignments. One common task is identification of ...
written 7 months ago by al-ash100
0
votes
4
answers
1.4k
views
4
answers
Answer: A: Make matrix of protein pairwise identities/similarities from multiple protein se
... I ended up with the following command line solution using clustal omega which converts distance matrix to percent identity matrix: clustalo-1.2.4-Ubuntu-x86_64 --full --percent-id --distmat-out=output.distmat -i input.aa.fa ...
written 7 months ago by al-ash100

Latest awards to al-ash

Popular Question 11 weeks ago, created a question with more than 1,000 views. For OrthoDB - How to retrieve ortholog groups for only the selected species
Popular Question 3 months ago, created a question with more than 1,000 views. For Entrez Direct E-utilities - using match and xtract to filter by data value
Popular Question 4 months ago, created a question with more than 1,000 views. For How to append strings (from one file) to Fasta headers (in another file)
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to trim nucleotide sequences to length divisible by 3
Popular Question 6 months ago, created a question with more than 1,000 views. For Entrez Direct E-utilities - using match and xtract to filter by data value
Popular Question 8 months ago, created a question with more than 1,000 views. For "Optimal" setting of CPU and max_memory in Trinity
Popular Question 13 months ago, created a question with more than 1,000 views. For How to append strings (from one file) to Fasta headers (in another file)
Popular Question 14 months ago, created a question with more than 1,000 views. For Entrez Direct E-utilities - using match and xtract to filter by data value
Scholar 17 months ago, created an answer that has been accepted. For A: How to trim nucleotide sequences to length divisible by 3
Scholar 18 months ago, created an answer that has been accepted. For A: How to trim nucleotide sequences to length divisible by 3
Popular Question 22 months ago, created a question with more than 1,000 views. For How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
Supporter 22 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2128 users visited in the last hour