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4.4k
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Comment: Comment: Metabolomics log-transform or standardize for WGCNA
9 weeks ago by DNAlias ▴ 40
2
votes
1
reply
900
views
Using OrthoMCL on command line
orthomcl
updated 2.8 years ago by 14k • written 2.8 years ago by ▴ 40
0
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0
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475
views
PAML/CODEML: which sites are selected in site model?
paml codeml
3.0 years ago by DNAlias ▴ 40
0
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0
replies
520
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PAML (CODEML) with 0 branch lengths
PAML codeml
3.0 years ago by DNAlias ▴ 40
1
vote
0
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704
views
Codon alignment with degenerate nucleotides?
paml codeml codon alignment
3.0 years ago by DNAlias ▴ 40
1
vote
4
replies
1.3k
views
Finding transcriptome coverage of genome
mapping transcriptome trinity RNAseq
updated 3.1 years ago by ▴ 660 • written 3.1 years ago by ▴ 40
0
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0
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545
views
Augustus training with partial transcriptome?
augustus maker maker2 annotation
3.1 years ago by DNAlias ▴ 40
2
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1
reply
1.3k
views
What are the best intron splice finder tools?
intron gene prediction eukaryotes annotation
3.6 years ago by DNAlias ▴ 40
0
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0
replies
600
views
Comment: A: Translation for genes with introns
3.6 years ago by DNAlias ▴ 40
0
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1
reply
600
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Translation for genes with introns
translation eukaryote
3.6 years ago by DNAlias ▴ 40
0
votes
1
reply
734
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Is there a way to limit the number of returned efetch (text, tabular) terms with just the entrez api (not entrez direct)
entrez eutils ncbi
3.7 years ago by DNAlias ▴ 40
0
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1
reply
823
views
What does it mean when a gene has an exon count of 0 on the ncbi database?
ncbi introns
3.7 years ago by DNAlias ▴ 40
0
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1
reply
849
views
Comment: C: What is the best way to get a set of all of the genes for a genome via entrez?
3.7 years ago by DNAlias ▴ 40
3
votes
3
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849
views
What is the best way to get a set of all of the genes for a genome via entrez?
entrez
updated 3.7 years ago by 142k • written 3.7 years ago by ▴ 40
5
votes
1
reply
1.3k
views
RAxML: comparing ML values
raxml
updated 3.8 years ago by 20 • written 4.4 years ago by ▴ 40
0
votes
2
replies
618
views
Retrieving assembly scaffold length information without downloading the sequence?
Assembly
3.9 years ago by DNAlias ▴ 40
0
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0
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840
views
ClustalW output MSA in R (without consensus)
msa R
4.0 years ago by DNAlias ▴ 40
4
votes
7
replies
3.6k
views
Clarification for using PSI-BLAST to generate a PSSM (am I doing it right?)
psiblast
updated 4.0 years ago by ★ 27k • written 4.0 years ago by ▴ 40
0
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0
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3.6k
views
Comment: C: Clarification for using PSI-BLAST to generate a PSSM (am I doing it right?)
4.0 years ago by DNAlias ▴ 40
0
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0
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849
views
Comment: C: Is there a way to use API to convert taxa-ID to common/scientific name via NCBI?
4.0 years ago by DNAlias ▴ 40
1
vote
4
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849
views
Is there a way to use API to convert taxa-ID to common/scientific name via NCBI?
ncbi api
4.0 years ago by DNAlias ▴ 40
0
votes
2
replies
605
views
Does the MAKER pipeline require transcriptional data?
maker annotation
updated 4.0 years ago by 15k • written 4.0 years ago by ▴ 40
0
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0
replies
593
views
OrthoDB API: accessing hierarchical taxonomy data using R
orthodb
4.0 years ago by DNAlias ▴ 40
0
votes
1
reply
797
views
Comment: C: What programs can be used to predict all of the coding sequences in a eukaryotic
4.0 years ago by DNAlias ▴ 40
2
votes
1
reply
497
views
What phylogenetic groupings are used for busco4?
phylogenetics
updated 4.1 years ago by ★ 27k • written 4.1 years ago by ▴ 40
3
votes
6
replies
797
views
What programs can be used to predict all of the coding sequences in a eukaryotic genome?
genome
4.1 years ago by DNAlias ▴ 40
0
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0
replies
3.0k
views
Comment: C: How to generate a multiple sequence alignment that retains the annotations from
4.3 years ago by DNAlias ▴ 40
0
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0
replies
3.0k
views
Comment: C: How to generate a multiple sequence alignment that retains the annotations from
4.3 years ago by DNAlias ▴ 40
0
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3
replies
3.0k
views
Comment: C: How to generate a multiple sequence alignment that retains the annotations from
4.3 years ago by DNAlias ▴ 40
2
votes
5
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3.0k
views
How to generate a multiple sequence alignment that retains the annotations from the original sequences?
sequence alignment
updated 4.3 years ago by ★ 27k • written 4.3 years ago by ▴ 40
0
votes
0
replies
704
views
calculating unassembled insert size mean/SD/min/max from PE library
genome Assembly
4.3 years ago by DNAlias ▴ 40
0
votes
2
replies
784
views
Non-de bruijn graph assemblers
Assembly
4.3 years ago by DNAlias ▴ 40
1
vote
1
reply
844
views
How are haplotypes/heterozygosity resolved in sequence assembly?
assembly
updated 4.3 years ago by ★ 2.5k • written 4.4 years ago by ▴ 40
3
votes
2
replies
660
views
What makes certain genomes harder to sequence? Are there any trends among taxonomic groups?
sequencing next-gen
updated 4.4 years ago by ★ 27k • written 4.4 years ago by ▴ 40
0
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1
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4.2k
views
Comment: C: How to download genome via Entrez
4.6 years ago by DNAlias ▴ 40
3
votes
4
replies
4.2k
views
How to download genome via Entrez
entrez fetch ncbi
updated 4.6 years ago by ▴ 600 • written 4.6 years ago by ▴ 40
0
votes
2
replies
775
views
Generating a list of all GI numbers for a genome
NCBI
updated 4.6 years ago by ▴ 10 • written 4.6 years ago by ▴ 40
2
votes
1
reply
2.0k
views
When to use masking in BLAST?
BLAST masking
4.6 years ago by DNAlias ▴ 40
2
votes
2
replies
2.9k
views
MrBayes batch scripting
mrbayes bash
updated 4.6 years ago by ★ 27k • written 4.6 years ago by ▴ 40
1
vote
0
replies
811
views
MrBayes: placing a new branch on an existing tree
mrbayes phylogenetics
4.6 years ago by DNAlias ▴ 40
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