Bioinformatics Stack Exchange

3

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1

answer

55

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For phylogenetic tree construction from core-genome which one is preferable: amino-acid based MSA or nucleotide based MSA?

alignment sequence-alignment fasta phylogenetics phylogeny

modified Mar 17 at 10:35 Michael 3,373

2

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1

answer

34

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Translating a genome sequence into possible frames

alignment sequencing proteins blast ncbi

modified Mar 15 at 10:36 Michael 3,373

0

votes

0

answers

26

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Given a multiple sequence alignment, how do I output all of the non-consensus characters by location?

alignment sequence-alignment

modified Mar 5 at 3:22 EB2127 1,253

1

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1

answer

37

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choosing a good representative genome subset

alignment clustering subset

answered Mar 3 at 14:27 Peter Menzel 383

5

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2

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113

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Counting letters in phylip alignment columns with Biopython

alignment phylogenetics biopython phylogeny phylip

modified Feb 22 at 15:31 Michael 3,373

1

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2

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334

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How BWA generate index files?

alignment sequence-alignment bwa

modified Feb 18 at 23:42 jay 11

2

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3

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77

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Make a fasta out of mapped reads without taking into account the reference

alignment bam

answered Feb 13 at 12:50 Stuber 161

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1

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17

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Running tophat dockerfile in background

alignment bash docker

answered Feb 13 at 7:10 Devon Ryan♦ 16.4k

1

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1

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79

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Read alignment using Bowtie2

alignment bowtie2 crispr

modified Feb 9 at 15:01 Community♦ 1

2

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1

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605

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How do I find split reads?

alignment bam structural-variation cigar

modified Jan 26 at 20:03 Community♦ 1

12

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2

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5k

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Meaning of BWA-MEM MAPQ scores

alignment read-mapping bwa sequence-alignment

modified Jan 4 at 4:21 gringer 9,010

2

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1

answer

40

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How can I not show insertions in the Integrative Genome Viewer (IGV)?

alignment sequence-alignment visualization igv

modified Jan 3 at 18:04 charlesdarwin 2,253

0

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1

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26

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Use of Electronic Phenotype in EHR

alignment database genome statistics machine-learning

answered Dec 25 '19 at 20:29 Devon Ryan♦ 16.4k

2

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2

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666

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Error while calling bcftools mpileup - Failed to open -: unknown file type

alignment bam vcf samtools nanopore

modified Dec 6 '19 at 16:02 Community♦ 1

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For phylogenetic tree construction from core-genome which one is preferable: amino-acid based MSA or nucleotide based MSA?

Translating a genome sequence into possible frames

Given a multiple sequence alignment, how do I output all of the non-consensus characters by location?

choosing a good representative genome subset

Counting letters in phylip alignment columns with Biopython

How BWA generate index files?

Make a fasta out of mapped reads without taking into account the reference

Running tophat dockerfile in background

Read alignment using Bowtie2

How do I find split reads?

Meaning of BWA-MEM MAPQ scores

How can I not show insertions in the Integrative Genome Viewer (IGV)?

Use of Electronic Phenotype in EHR

Error while calling bcftools mpileup - Failed to open -: unknown file type

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