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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 19 months ago by • 0 • written 2.5 years ago by ▴ 210
1
vote
1
reply
981
views
Retrieve all annotated features in a GenBank record
efetch edirect genbank feature annotations
4.7 years ago by al-ash ▴ 210
4
votes
6
replies
9.2k
views
Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
Entrez Direct E-utilities efetch CDS retrieve
4.7 years ago by al-ash ▴ 210
2
votes
3
replies
7.3k
views
How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
HISAT2 gtf gff stringtie
updated 4.9 years ago by 20 • written 8.4 years ago by ▴ 210
1
vote
3
replies
1.3k
views
Submitting many transcriptomes to TSA - how to automatize?
TSA transcriptome NCBI database submition
5.8 years ago by al-ash ▴ 210
0
votes
2
replies
5.8k
views
OrthoDB - How to retrieve ortholog groups for only the selected species
OrthoDB JSON API ortholog
updated 5.9 years ago by • 0 • written 8.2 years ago by ▴ 210
0
votes
2
replies
2.1k
views
Generate all possible bifurkating newick trees for N taxa
newick tree generate
6.3 years ago by al-ash ▴ 210
0
votes
2
replies
2.9k
views
Combine node/branch labels from multiple trees into one
TreeGraph2 tree annotation label
6.4 years ago by al-ash ▴ 210
6
votes
11
replies
15k
views
Make matrix of protein pairwise identities/similarities from multiple protein sequences
pairwise protein identity similarity matrix
updated 3.4 years ago by • 0 • written 7.2 years ago by ▴ 210
1
vote
1
reply
2.5k
views
Compare topologies of trees with non-identical tip labels
R dendextend tanglegram tree topology
updated 6.8 years ago by ★ 3.0k • written 6.9 years ago by ▴ 210
1
vote
1
reply
3.0k
views
Trimmomatic adapter clipping removes many reads even if "keepBothReads" parameter is selected
Trimmomatic pair-end Illumina adapter trimming
updated 6.9 years ago by 16k • written 7.0 years ago by ▴ 210
3
votes
7
replies
5.7k
views
Tune criteria for extraction of consensus sequence from bam/sam alignment
bam sam consensus bcftools vcfutils
7.3 years ago by al-ash ▴ 210
4
votes
2
replies
3.5k
views
How to trim nucleotide sequences to length divisible by 3
awk incomplete codon
7.4 years ago by al-ash ▴ 210
2
votes
2
replies
1.8k
views
Map eukaryotic genomic reads to transcript reference of closely related organism
RNA-Seq splice-aware splice-unaware mapping reads
updated 7.4 years ago by ▴ 50 • written 7.4 years ago by ▴ 210
1
vote
7
replies
5.5k
views
"Optimal" setting of CPU and max_memory in Trinity
Trinity CPU RAM
updated 8.1 years ago by ▴ 10 • written 8.3 years ago by ▴ 210
1
vote
2
replies
2.2k
views
InterProScan standalone - error connected to non-unique fasta identifiers
InterProScan nucleic acid non-unique identifier
8.3 years ago by al-ash ▴ 210
2
votes
4
replies
4.6k
views
Entrez Direct E-utilities - using match and xtract to filter by data value
Entrez Direct E-utilities match xtract
updated 8.5 years ago by ▴ 330 • written 8.6 years ago by ▴ 210
10
votes
9
replies
6.6k
views
How to append strings (from one file) to Fasta headers (in another file)
bioawk FASTA header append
updated 8.7 years ago by 22k • written 8.7 years ago by ▴ 210
4
votes
3
replies
5.6k
views
Batch download of protein FASTAs from GenBank using a list (>100) of protein accessions
genbank FASTA E-utils
updated 8.7 years ago by ▴ 40 • written 8.7 years ago by ▴ 210
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