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Importing nexus-formatted tree (e.g. BEAST tree) into R as a phylo object with node labels
BEAST nexus phylo treedata R
updated 6 months ago by • 0 • written 17 months ago by ▴ 200
1
vote
1
reply
781
views
Retrieve all annotated features in a GenBank record
efetch edirect genbank feature annotations
3.6 years ago by al-ash ▴ 200
4
votes
6
replies
8.4k
views
Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
Entrez Direct E-utilities efetch CDS retrieve
3.6 years ago by al-ash ▴ 200
2
votes
3
replies
6.9k
views
How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
HISAT2 gtf gff stringtie
updated 3.8 years ago by 20 • written 7.4 years ago by ▴ 200
1
vote
3
replies
988
views
Submitting many transcriptomes to TSA - how to automatize?
TSA transcriptome NCBI database submition
4.7 years ago by al-ash ▴ 200
0
votes
2
replies
5.2k
views
OrthoDB - How to retrieve ortholog groups for only the selected species
OrthoDB JSON API ortholog
updated 4.9 years ago by • 0 • written 7.1 years ago by ▴ 200
0
votes
2
replies
1.8k
views
Generate all possible bifurkating newick trees for N taxa
newick tree generate
5.2 years ago by al-ash ▴ 200
0
votes
2
replies
2.6k
views
Combine node/branch labels from multiple trees into one
TreeGraph2 tree annotation label
5.4 years ago by al-ash ▴ 200
6
votes
11
replies
13k
views
Make matrix of protein pairwise identities/similarities from multiple protein sequences
pairwise protein identity similarity matrix
updated 2.3 years ago by • 0 • written 6.2 years ago by ▴ 200
1
vote
1
reply
2.1k
views
Compare topologies of trees with non-identical tip labels
R dendextend tanglegram tree topology
updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 200
1
vote
1
reply
2.7k
views
Trimmomatic adapter clipping removes many reads even if "keepBothReads" parameter is selected
Trimmomatic pair-end Illumina adapter trimming
updated 5.8 years ago by 16k • written 5.9 years ago by ▴ 200
3
votes
7
replies
4.9k
views
Tune criteria for extraction of consensus sequence from bam/sam alignment
bam sam consensus bcftools vcfutils
6.3 years ago by al-ash ▴ 200
3
votes
2
replies
3.0k
views
How to trim nucleotide sequences to length divisible by 3
awk incomplete codon
6.3 years ago by al-ash ▴ 200
2
votes
2
replies
1.6k
views
Map eukaryotic genomic reads to transcript reference of closely related organism
RNA-Seq splice-aware splice-unaware mapping reads
updated 6.4 years ago by ▴ 50 • written 6.4 years ago by ▴ 200
1
vote
7
replies
4.7k
views
"Optimal" setting of CPU and max_memory in Trinity
Trinity CPU RAM
updated 7.0 years ago by • 0 • written 7.2 years ago by ▴ 200
1
vote
2
replies
1.9k
views
InterProScan standalone - error connected to non-unique fasta identifiers
InterProScan nucleic acid non-unique identifier
7.3 years ago by al-ash ▴ 200
2
votes
4
replies
4.0k
views
Entrez Direct E-utilities - using match and xtract to filter by data value
Entrez Direct E-utilities match xtract
updated 7.4 years ago by ▴ 330 • written 7.5 years ago by ▴ 200
10
votes
9
replies
5.6k
views
How to append strings (from one file) to Fasta headers (in another file)
bioawk FASTA header append
updated 7.6 years ago by 21k • written 7.6 years ago by ▴ 200
4
votes
3
replies
4.9k
views
Batch download of protein FASTAs from GenBank using a list (>100) of protein accessions
genbank FASTA E-utils
updated 7.7 years ago by ▴ 40 • written 7.7 years ago by ▴ 200
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