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questions
2
votes
1
reply
893
views
Using OrthoMCL on command line
orthomcl
updated 2.8 years ago by
dariober
14k • written 2.8 years ago by
DNAlias
▴ 40
0
votes
0
replies
471
views
PAML/CODEML: which sites are selected in site model?
paml
codeml
3.0 years ago by
DNAlias
▴ 40
0
votes
0
replies
515
views
PAML (CODEML) with 0 branch lengths
PAML
codeml
3.0 years ago by
DNAlias
▴ 40
1
vote
0
replies
697
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 3.0 years ago by
prasundutta87
▴ 660 • written 3.0 years ago by
DNAlias
▴ 40
0
votes
0
replies
542
views
Augustus training with partial transcriptome?
augustus
maker
maker2
annotation
3.1 years ago by
DNAlias
▴ 40
2
votes
1
reply
1.3k
views
What are the best intron splice finder tools?
intron
gene prediction
eukaryotes
annotation
3.5 years ago by
DNAlias
▴ 40
0
votes
1
reply
595
views
Translation for genes with introns
translation
eukaryote
3.5 years ago by
DNAlias
▴ 40
0
votes
1
reply
726
views
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
3.6 years ago by
DNAlias
▴ 40
0
votes
1
reply
813
views
What does it mean when a gene has an exon count of 0 on the ncbi database?
ncbi
introns
3.6 years ago by
DNAlias
▴ 40
3
votes
3
replies
843
views
What is the best way to get a set of all of the genes for a genome via entrez?
entrez
updated 3.6 years ago by
GenoMax
141k • written 3.6 years ago by
DNAlias
▴ 40
5
votes
1
reply
1.3k
views
RAxML: comparing ML values
raxml
updated 3.7 years ago by
Biostar
20 • written 4.4 years ago by
DNAlias
▴ 40
0
votes
2
replies
614
views
Retrieving assembly scaffold length information without downloading the sequence?
Assembly
3.9 years ago by
DNAlias
▴ 40
0
votes
0
replies
838
views
ClustalW output MSA in R (without consensus)
msa
R
3.9 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 3.9 years ago by
Mensur Dlakic
★ 27k • written 3.9 years ago by
DNAlias
▴ 40
1
vote
4
replies
838
views
Is there a way to use API to convert taxa-ID to common/scientific name via NCBI?
ncbi
api
3.9 years ago by
DNAlias
▴ 40
0
votes
2
replies
602
views
Does the MAKER pipeline require transcriptional data?
maker
annotation
updated 4.0 years ago by
lieven.sterck
15k • written 4.0 years ago by
DNAlias
▴ 40
0
votes
0
replies
588
views
OrthoDB API: accessing hierarchical taxonomy data using R
orthodb
4.0 years ago by
DNAlias
▴ 40
2
votes
1
reply
492
views
What phylogenetic groupings are used for busco4?
phylogenetics
updated 4.0 years ago by
Mensur Dlakic
★ 27k • written 4.0 years ago by
DNAlias
▴ 40
3
votes
6
replies
788
views
What programs can be used to predict all of the coding sequences in a eukaryotic genome?
genome
4.0 years ago by
DNAlias
▴ 40
2
votes
5
replies
2.9k
views
How to generate a multiple sequence alignment that retains the annotations from the original sequences?
sequence alignment
updated 4.2 years ago by
Mensur Dlakic
★ 27k • written 4.2 years ago by
DNAlias
▴ 40
0
votes
0
replies
700
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
775
views
Non-de bruijn graph assemblers
Assembly
4.3 years ago by
DNAlias
▴ 40
1
vote
1
reply
837
views
How are haplotypes/heterozygosity resolved in sequence assembly?
assembly
updated 4.3 years ago by
Vitis
★ 2.5k • written 4.3 years ago by
DNAlias
▴ 40
3
votes
2
replies
654
views
What makes certain genomes harder to sequence? Are there any trends among taxonomic groups?
sequencing
next-gen
updated 4.3 years ago by
Mensur Dlakic
★ 27k • written 4.3 years ago by
DNAlias
▴ 40
3
votes
4
replies
4.2k
views
How to download genome via Entrez
entrez
fetch
ncbi
updated 4.5 years ago by
massa.kassa.sc3na
▴ 600 • written 4.5 years ago by
DNAlias
▴ 40
0
votes
2
replies
773
views
Generating a list of all GI numbers for a genome
NCBI
updated 4.6 years ago by
yehchan57
▴ 10 • written 4.6 years ago by
DNAlias
▴ 40
2
votes
1
reply
1.9k
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
Mensur Dlakic
★ 27k • written 4.6 years ago by
DNAlias
▴ 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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