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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 13 months ago by • 0 • written 2.1 years ago by ▴ 210
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0
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7.1k
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Answer: Answer: stand alone blast display header in output file (customizing -outfmt 6)
2.3 years ago by al-ash ▴ 210
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0
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7.1k
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Comment: Comment: stand alone blast display header in output file (customizing -outfmt 6)
2.3 years ago by al-ash ▴ 210
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0
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1.4k
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Answer: Answer: Submitting phage sequences to NCBI
2.8 years ago by al-ash ▴ 210
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0
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19k
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Comment: Comment: Is There A Faster Replacement For Fastq-Dump (From The Sra-Toolkit)?
3.4 years ago by al-ash ▴ 210
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1
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863
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Retrieve all annotated features in a GenBank record
efetch edirect genbank feature annotations
4.2 years ago by al-ash ▴ 210
4
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6
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8.8k
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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
4.2 years ago by al-ash ▴ 210
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0
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3.2k
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Answer: A: QIIME cannot run python script
4.4 years ago by al-ash ▴ 210
2
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3
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7.1k
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How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
HISAT2 gtf gff stringtie
updated 4.4 years ago by 20 • written 8.0 years ago by ▴ 210
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0
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1.9k
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Comment: C: Appropriateness of using topology constraints to enforce species tree concordant
4.8 years ago by al-ash ▴ 210
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0
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17k
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Comment: C: Downloading Data From Mg-Rast
4.8 years ago by al-ash ▴ 210
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0
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89k
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Comment: C: Sequence Length Distribution From A Fastq File
5.2 years ago by al-ash ▴ 210
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0
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2.2k
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Comment: C: Unable to perform tbl2asn for submission of transcriptome to Genbank
5.3 years ago by al-ash ▴ 210
0
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1
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1.1k
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Comment: C: Submitting many transcriptomes to TSA - how to automatize?
5.3 years ago by al-ash ▴ 210
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3
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1.1k
views
Submitting many transcriptomes to TSA - how to automatize?
TSA transcriptome NCBI database submition
5.3 years ago by al-ash ▴ 210
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2
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5.5k
views
OrthoDB - How to retrieve ortholog groups for only the selected species
OrthoDB JSON API ortholog
updated 5.5 years ago by • 0 • written 7.7 years ago by ▴ 210
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2
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103k
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Comment: C: Multiline Fasta To Single Line Fasta
5.7 years ago by al-ash ▴ 210
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0
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4.8k
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Comment: A: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
5.8 years ago by al-ash ▴ 210
0
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0
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39k
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Comment: C: BLAST, setting maximum number of hits
updated 5.8 years ago by 44k • written 6.7 years ago by ▴ 210
0
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0
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8.2k
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Comment: C: SRX from SRR IDs
5.8 years ago by al-ash ▴ 210
0
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2
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1.9k
views
Generate all possible bifurkating newick trees for N taxa
newick tree generate
5.8 years ago by al-ash ▴ 210
0
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1
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6.9k
views
Comment: C: [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
6.0 years ago by al-ash ▴ 210
0
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0
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1.9k
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Comment: C: Generate all bifurkating newick trees given for N taxa
6.0 years ago by al-ash ▴ 210
0
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0
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2.7k
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Comment: C: Combine node/branch labels from multiple trees into one
6.0 years ago by al-ash ▴ 210
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2
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2.7k
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Combine node/branch labels from multiple trees into one
TreeGraph2 tree annotation label
6.0 years ago by al-ash ▴ 210
0
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0
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4.9k
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Answer: A: yn00 in PAML returns error: Error in sequence data file: E at 3 seq 1.
6.0 years ago by al-ash ▴ 210
2
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1
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10k
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Answer: A: Manual edit of multiple alignment
6.0 years ago by al-ash ▴ 210
1
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2
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14k
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Answer: A: Make matrix of protein pairwise identities/similarities from multiple protein se
6.1 years ago by al-ash ▴ 210
6
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11
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14k
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Make matrix of protein pairwise identities/similarities from multiple protein sequences
pairwise protein identity similarity matrix
updated 2.9 years ago by • 0 • written 6.8 years ago by ▴ 210
0
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0
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3.2k
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Comment: C: Platanus assembler : unable to start contig assembly, any problem with the comma
6.2 years ago by al-ash ▴ 210
1
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1
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2.3k
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Compare topologies of trees with non-identical tip labels
R dendextend tanglegram tree topology
updated 6.4 years ago by ★ 3.0k • written 6.4 years ago by ▴ 210
1
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1
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2.8k
views
Trimmomatic adapter clipping removes many reads even if "keepBothReads" parameter is selected
Trimmomatic pair-end Illumina adapter trimming
updated 6.4 years ago by 16k • written 6.5 years ago by ▴ 210
1
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1
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5.9k
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Comment: C: Species tree vs Gene trees during evolutionary analyses: Does it matter?
6.7 years ago by al-ash ▴ 210
2
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0
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4.1k
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Answer: A: Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
6.7 years ago by al-ash ▴ 210
0
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0
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12k
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Comment: C: Unrooting Trees Help
6.7 years ago by al-ash ▴ 210
0
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0
replies
6.9k
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Comment: C: [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
6.8 years ago by al-ash ▴ 210
1
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1
reply
14k
views
Comment: C: Make matrix of protein pairwise identities/similarities from multiple protein se
6.8 years ago by al-ash ▴ 210
0
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1
reply
14k
views
Comment: C: Make matrix of protein pairwise identities/similarities from multiple protein se
6.8 years ago by al-ash ▴ 210
3
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7
replies
5.3k
views
Tune criteria for extraction of consensus sequence from bam/sam alignment
bam sam consensus bcftools vcfutils
6.9 years ago by al-ash ▴ 210
2
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1
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5.3k
views
Answer: A: Tune criteria for extraction of consensus sequence from bam/sam alignment
6.9 years ago by al-ash ▴ 210
0
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1
reply
5.3k
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Comment: C: Tune criteria for extraction of consensus sequence from bam/sam alignment
6.9 years ago by al-ash ▴ 210
0
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1
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5.3k
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Comment: C: Tune criteria for extraction of consensus sequence from bam/sam alignment
6.9 years ago by al-ash ▴ 210
1
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0
replies
19k
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Comment: C: gff3 to CDS fasta
6.9 years ago by al-ash ▴ 210
0
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0
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6.4k
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Answer: A: Pyfasta Split By Header
6.9 years ago by al-ash ▴ 210
4
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1
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3.2k
views
Answer: A: How to trim nucleotide sequences to length divisible by 3
6.9 years ago by al-ash ▴ 210
4
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2
replies
3.2k
views
How to trim nucleotide sequences to length divisible by 3
awk incomplete codon
6.9 years ago by al-ash ▴ 210
0
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0
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8.1k
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Comment: C: Preventing EMBOSS transeq from renaming sequences
6.9 years ago by al-ash ▴ 210
0
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0
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5.6k
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Answer: A: Mira 4 Mapping Error
7.0 years ago by al-ash ▴ 210
0
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0
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8.5k
views
Comment: C: BAM format file to FASTA alignment file
7.0 years ago by al-ash ▴ 210
0
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0
replies
50k
views
Comment: Comment: Reference Assembly - Mapping Reads To A Reference Genome
updated 22 months ago by 44k • written 7.0 years ago by ▴ 210
79 results • Page 1 of 2
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