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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
11 months ago by al-ash ▴ 200
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5.9k
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Answer: Answer: stand alone blast display header in output file (customizing -outfmt 6)
13 months ago by al-ash ▴ 200
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5.9k
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Comment: Comment: stand alone blast display header in output file (customizing -outfmt 6)
13 months ago by al-ash ▴ 200
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0
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897
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Answer: Answer: Submitting phage sequences to NCBI
20 months ago by al-ash ▴ 200
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0
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17k
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Comment: Comment: Is There A Faster Replacement For Fastq-Dump (From The Sra-Toolkit)?
2.2 years ago by al-ash ▴ 200
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1
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682
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Retrieve all annotated features in a GenBank record
efetch edirect genbank feature annotations
3.1 years ago by al-ash ▴ 200
4
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6
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7.8k
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Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
Entrez Direct E-utilities efetch CDS retrieve
3.1 years ago by al-ash ▴ 200
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2.9k
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Answer: A: QIIME cannot run python script
3.2 years ago by al-ash ▴ 200
2
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3
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6.7k
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How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
HISAT2 gtf gff stringtie
updated 3.3 years ago by 20 • written 6.8 years ago by ▴ 200
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1.6k
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Comment: C: Appropriateness of using topology constraints to enforce species tree concordant
3.6 years ago by al-ash ▴ 200
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16k
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Comment: C: Downloading Data From Mg-Rast
3.6 years ago by al-ash ▴ 200
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0
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80k
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Comment: C: Sequence Length Distribution From A Fastq File
4.1 years ago by al-ash ▴ 200
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0
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1.9k
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Comment: C: Unable to perform tbl2asn for submission of transcriptome to Genbank
4.1 years ago by al-ash ▴ 200
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1
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850
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Comment: C: Submitting many transcriptomes to TSA - how to automatize?
4.1 years ago by al-ash ▴ 200
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3
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850
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Submitting many transcriptomes to TSA - how to automatize?
TSA transcriptome NCBI database submition
4.1 years ago by al-ash ▴ 200
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2
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4.9k
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OrthoDB - How to retrieve ortholog groups for only the selected species
OrthoDB JSON API ortholog
updated 4.3 years ago by • 0 • written 6.6 years ago by ▴ 200
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2
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92k
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Comment: C: Multiline Fasta To Single Line Fasta
4.5 years ago by al-ash ▴ 200
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0
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4.3k
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Comment: A: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
4.6 years ago by al-ash ▴ 200
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0
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35k
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Comment: C: BLAST, setting maximum number of hits
updated 4.6 years ago by 40k • written 5.5 years ago by ▴ 200
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0
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7.3k
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Comment: C: SRX from SRR IDs
4.6 years ago by al-ash ▴ 200
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2
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1.6k
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Generate all possible bifurkating newick trees for N taxa
newick tree generate
4.7 years ago by al-ash ▴ 200
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1
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5.8k
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Comment: C: [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
4.8 years ago by al-ash ▴ 200
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0
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1.6k
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Comment: C: Generate all bifurkating newick trees given for N taxa
4.8 years ago by al-ash ▴ 200
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2.4k
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Comment: C: Combine node/branch labels from multiple trees into one
4.8 years ago by al-ash ▴ 200
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2
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2.4k
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Combine node/branch labels from multiple trees into one
TreeGraph2 tree annotation label
4.8 years ago by al-ash ▴ 200
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0
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4.2k
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Answer: A: yn00 in PAML returns error: Error in sequence data file: E at 3 seq 1.
4.8 years ago by al-ash ▴ 200
2
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1
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8.6k
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Answer: A: Manual edit of multiple alignment
4.9 years ago by al-ash ▴ 200
1
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2
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11k
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Answer: A: Make matrix of protein pairwise identities/similarities from multiple protein se
4.9 years ago by al-ash ▴ 200
6
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11
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11k
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Make matrix of protein pairwise identities/similarities from multiple protein sequences
pairwise protein identity similarity matrix
updated 21 months ago by • 0 • written 5.6 years ago by ▴ 200
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0
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2.9k
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Comment: C: Platanus assembler : unable to start contig assembly, any problem with the comma
5.0 years ago by al-ash ▴ 200
1
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1
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2.0k
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Compare topologies of trees with non-identical tip labels
R dendextend tanglegram tree topology
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 200
1
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1
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2.5k
views
Trimmomatic adapter clipping removes many reads even if "keepBothReads" parameter is selected
Trimmomatic pair-end Illumina adapter trimming
updated 5.2 years ago by 16k • written 5.3 years ago by ▴ 200
1
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1
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4.9k
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Comment: C: Species tree vs Gene trees during evolutionary analyses: Does it matter?
5.5 years ago by al-ash ▴ 200
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3.7k
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Answer: A: Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
5.5 years ago by al-ash ▴ 200
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0
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11k
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Comment: C: Unrooting Trees Help
5.5 years ago by al-ash ▴ 200
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0
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5.8k
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Comment: C: [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
5.6 years ago by al-ash ▴ 200
1
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1
reply
11k
views
Comment: C: Make matrix of protein pairwise identities/similarities from multiple protein se
5.6 years ago by al-ash ▴ 200
0
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1
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11k
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Comment: C: Make matrix of protein pairwise identities/similarities from multiple protein se
5.6 years ago by al-ash ▴ 200
2
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1
reply
4.6k
views
Answer: A: Tune criteria for extraction of consensus sequence from bam/sam alignment
5.7 years ago by al-ash ▴ 200
3
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7
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4.6k
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Tune criteria for extraction of consensus sequence from bam/sam alignment
bam sam consensus bcftools vcfutils
5.7 years ago by al-ash ▴ 200
0
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1
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4.6k
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Comment: C: Tune criteria for extraction of consensus sequence from bam/sam alignment
5.7 years ago by al-ash ▴ 200
0
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1
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4.6k
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Comment: C: Tune criteria for extraction of consensus sequence from bam/sam alignment
5.7 years ago by al-ash ▴ 200
1
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0
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16k
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Comment: C: gff3 to CDS fasta
5.7 years ago by al-ash ▴ 200
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0
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5.9k
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Answer: A: Pyfasta Split By Header
5.7 years ago by al-ash ▴ 200
3
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1
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2.8k
views
Answer: A: How to trim nucleotide sequences to length divisible by 3
5.8 years ago by al-ash ▴ 200
3
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2
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2.8k
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How to trim nucleotide sequences to length divisible by 3
awk incomplete codon
5.8 years ago by al-ash ▴ 200
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0
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7.1k
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Comment: C: Preventing EMBOSS transeq from renaming sequences
5.8 years ago by al-ash ▴ 200
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0
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5.1k
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Answer: A: Mira 4 Mapping Error
5.8 years ago by al-ash ▴ 200
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0
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7.9k
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Comment: C: BAM format file to FASTA alignment file
5.8 years ago by al-ash ▴ 200
0
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0
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48k
views
Comment: Comment: Reference Assembly - Mapping Reads To A Reference Genome
updated 7 months ago by 40k • written 5.8 years ago by ▴ 200
79 results • Page 1 of 2
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