All Questions
Tagged with phylip or phylogenetics
152 questions with no upvoted or accepted answers
5
votes
1
answer
258
views
UPGMA computation
The unweighted pair group method with arithmetic mean (UPGMA) is a hierarchical clustering method, for example used in phylogeny. In a phylogenetic tree it would result in a global molecular clock ...
5
votes
0
answers
270
views
convert supplementary reads to primary in sam or bam
I have a problem with a tool, that possibly ignores supplementary reads. I want to find out a bit how this tool works by converting all supplementary reads to primary reads, and then change the names ...
- 153
5
votes
0
answers
223
views
R Biostrings pairwiseAlignment to BAM
The R package Biostrings has a function to create a pairwiseAlignment from pattern and subject sequences.
So far I can save the result into a text file using writePairwiseAlignments. I would like to ...
- 151
5
votes
1
answer
2k
views
How to install DnaSP on a Mac
I need to install DnaSp, a nice GUI originally written for Windows for the population genetics of nucleotide sequence data.
However, its not working on my mac. I'm using wine to install it using these ...
4
votes
1
answer
85
views
Waterman-Smith-Beyer implementation in Python
I am working on a text aligner to help me get a better understanding of specific steps necessary to perform sequence alignment. So far, things have been going great but I noticed yesterday that my ...
4
votes
1
answer
37
views
Transposable elements in phylogenetics
I'm very new to phylogenetics and want to build a cladogram from mammal species using pseudogene fragments. The procedure is as follows:
Find several query sequences from Gallus gallus of the genes ...
- 41
4
votes
0
answers
257
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How to get phylogenetic tree from multiple genes?
I constructed a phylogenetic tree using a gene (example - secA). I had to gather the same gene sequence for all the required species from public database-NCBI and then constructed the tree after ...
- 73
4
votes
0
answers
1k
views
Kraken2 > OTU format > Phyloseq
A collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION.
I would like to make a tree if the data using a ...
- 41
3
votes
0
answers
28
views
Add or Simulate Noise in Short-Read Paired End Data
For a project I'm working on, I need to figure out how to model noise that may be happening in real genomes due to alignment errors, contamination, etc. Specifically, short-read paired-end data either ...
Suraj Rajendran
3
votes
0
answers
718
views
Aligning PacBio HiFi reads to reference genome using pbmm2
I am trying to align a yeast strain sequenced by PacBio HiFi reads to the reference genome S288C (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000146045.2/) using pbmm2 but for some reason I am ...
- 1,063
3
votes
0
answers
125
views
PSSM Matrix in PSI-BLAST
After running PSI-BLAST one obtains a profile matrix with this header:
A R N D C Q E G H I L K M F P S T W Y V
How does PSI-...
- 307
3
votes
2
answers
555
views
Can't load files into PopART
I am trying to create haplotype networks in PopART (Population genetics with Reticulated Trees*) which I have successfully done many times in the past.
Two weeks ago the program was working fine for ...
3
votes
0
answers
73
views
How are the values of prop.part() and prop.clades() calculated?
Consider the following dataset:
...
- 317
3
votes
0
answers
61
views
Trying to show the gaps of each seq on bio::Graphics after converting clustalw
I want a box representing each sequence, positioned as they are in the alignment and with gaps shown as breaks in the each box.
I've been having trouble for a while with this and have been trying to ...
2
votes
1
answer
31
views
How to adjust QIIME DADA2 parameters to avoid eliminating real sequences
I am working with sequence reads (acquired through MiSeq platform by Illumina) from a viral inoculum. I have already used FastP to merge paired-end reads and cut 5' and 3' ends to remove adapters and ...
2
votes
0
answers
21
views
Understanding the Impact of Parameter Adjustment in KMA Aligner for Gene Analysis
I am currently using the KMA aligner (k-mer alignment) from Clausen et al. (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2336-6) to analyze gene sequences (metagenomics) and ...
- 155
2
votes
0
answers
45
views
How to create a dataset of contact maps of homologous proteins?
Disclaimer: I am a machine learning researcher working on network science and want to use proteins to test an algorithm of mine using real-world data. My bioinformatics knowledge is minimal.
I need to ...
- 121
2
votes
1
answer
55
views
Salmon Multiple File SCRIPT giving error
Hi I am using Salmon quantitation for multiple fastq paired files using following code
...
- 61
2
votes
0
answers
280
views
Fst calculation from VCF files
I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and ...
- 21
2
votes
1
answer
64
views
Error importing Maximum Credibility Tree from BEAST into R using treeio's read.beast()
I've encountered an issue that I'm hoping someone can help with. I constructed a phylogenetic tree using BEAST1 and then extracted the Maximum Credibility Tree using treeannotator. I'm trying to ...
2
votes
0
answers
29
views
How come bigWigSummary shows coverage greater than 1 for some region of the genome?
I am running this command, using the UCSC utilities:
bigWigSummary -type=coverage ./galGal6.phastCons77way.bw chr4 25526708 25528708 1
to get phastCons77way ...
- 43
2
votes
0
answers
133
views
Phylogenetic tree from a large FASTA file
I want to create a phylogenetic tree using a 3.8MB FASTA file with ambiguous code. How can I perform multiple sequence alignment and the construction of phylogenetic tree with these ambiguous codes?
...
- 21
2
votes
1
answer
49
views
Parsimony-distance neighborhoods in tree space
I have the following question about the paper A parsimony-based metric for phylogenetic trees by V. Moulton and T. Wu.
In this paper, the authors define a "parsimony-distance" between ...
- 216
2
votes
0
answers
29
views
Why does segmasker modify headers?
When parsing NCBI BLAST+ segmasker output, I realized the program modifies almost every header containing these strings: ( or )...
- 247
2
votes
1
answer
405
views
How to calculate average BLOSUM62 scores?
I can understand the motive behind the BLOSUM62 matrix, this being a pairwise mutation matrix describing aggregate mutations between the 20 amino acids.
However how would you calculate the average ...
2
votes
0
answers
34
views
Is there a DNAWeaver How-to guide?
Recently I've been trying to use DNA Weaver for customized gene assembly design.
Although there is a web version that allows to perform some assembly examples, I've tried to replicate them with python ...
- 21
2
votes
0
answers
19
views
Calculate interval of flanking introns
I am looking for a easy way to calculate the intervals of flanking introns based on a transcript annotation file. I have chosen a very complicated method:
...
- 51
2
votes
0
answers
101
views
2
votes
0
answers
36
views
Alignment with inserts and keeping the indexing of ref seq intact
Parts of sequences are given below-
Reference sequence (pre-alignment):
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGT
...
- 145
2
votes
1
answer
116
views
Build tree to calculate beta diversity
I am trying to calculate beta diversity* using the UniFrac distance on my data, each sample having OTUs values.
To calculate it, I saw it required building a tree with percentages that represented the ...
- 21
2
votes
0
answers
110
views
How to change sequence format in my alignment file?
I have fasta file with alingned several sequences (from MUSCLE), when I open it (e.g. notepad++) they look like:
And I want dot format of identities like and then save it in txt file.
I failed ...
- 216
2
votes
0
answers
368
views
Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!
I am using Platanus-allee 2.2.2 for heterozygous genome (~500mb) assembly with Illumina short reads and PacBio reads input data.
I have the file contigs.fa from short reads but phasing step with ...
- 21
2
votes
0
answers
784
views
Cannot blast against specific NCBI databases
I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : https://ftp.ncbi.nlm.nih.gov/blast/db/. Files in ...
- 21
2
votes
1
answer
317
views
Read alignment using Bowtie2
So this is related to CRISPR-CAS9. I am working with off-target predictions for my thesis and was looking at all scientific papers related to CRISPR. I found one and decided to use their datasets. The ...
- 21
2
votes
0
answers
234
views
How snippy makes MSA-like aligned fasta output from multiple samples?
From the log file it seems snippy doesn't do assembly. It only does mapping:
fastq --> SAM --> BAM --> VCF --> consensus_seq/snps
But if multiple ...
- 377
2
votes
0
answers
325
views
How to get bootstrap support of phylogenetic tree?
I have used multiple sequences aligned file of protein data to generate a maximum parsimony tree, then I used the "bootstrap_trees(msa, times, tree_constructor)" ...
- 503
2
votes
0
answers
49
views
Does anyone have older versions of NT and 16s RNA DB from NCBI?
I am in search of past years' versions of NT and 16s databases from NCBI. I recently contacted NCBI about this and they replied:
Unfortunately, we do not archive past versions of the blast ...
- 265
2
votes
0
answers
211
views
Reproducing population structure from 1000 Genomes Data
I recently tried to reproduce population structure with 1000 Genomes Project data (Phase 3, 2504 people).
According to supplementary material,
To reduce the dataset, we used VCFtools to only keep ...
- 31
2
votes
0
answers
32
views
Alignment using secondary and tertiary features of DNA
I m trying to align different sequences of length not greater than 50 bp. Could I incorporate additional information such as stacking energy, entropy, bonds etc as additional criteria in the alignment?...
2
votes
1
answer
260
views
Merging ssu-align alignments
ssu-align is an HMM-based MSA tool for ribosome's small subunit (SSU) sequences. It's bundled with three SSU models:
archaeal,
bacterial
eukaryotic
Approach Given a set of archaeal and ...
- 79
1
vote
0
answers
19
views
Metabolite function from DNA sequences
I have an aligned metagenome fasta file. I want to see the relation between the aligned genes and the so-called Clusters of Orthologous Groups (COGs). For the purpose of the analysis I am using the ...
- 11
1
vote
1
answer
21
views
How to identify a bacterium species from its short RNA-seq transcriptomics data?
I am new to RNA-seq analysis and wanted to ask if there is a method to reliably identify the species of a microbial organism using only its raw short RNA transcriptomics data. Here are some of the ...
- 69
1
vote
0
answers
29
views
Guidance Required on Prioritizing Columns for Gene Expression Analysis Using KMA Tool
I am currently in the process of comparing two distinct sets of genes that have been sequenced under two different conditions.
My objective is to ascertain whether the expression of specific genes in ...
- 155
1
vote
0
answers
40
views
Problems with pbmm2 alignment after subsampling
I have tested pbmm2 align on my total set of reads. However, the alignments are poor. Therefore I am trying to optimize the parameters with a few of them. After doing a subsampling with samtools -s 0,...
- 189
1
vote
0
answers
30
views
1
vote
0
answers
37
views
How to compare CDS, CNE, miRNA, UCNE across new related genomes?
I have 5 sets of raw Illumina whole genome shotgun data from 5 different species, and 3 reference genomes that are assembled/annotated, I want to produce a similar table to Table S2 of this paper: ...
- 101
1
vote
1
answer
58
views
Arbovirus phylogenetic analysis using the BEAST2 software via a global clock model
How do I perform a global clock phylogenetic analysis of an arbovirus using the BEAST2 software. If I intend to utilize the global clock model for analysis, kindly guide how to set the parameters of ...
- 11
1
vote
0
answers
25
views
Biopython PhyloTree to PyVis Network
We are trying to convert a Phylogenetic tree to networkx previously calculated with
...
- 195
1
vote
0
answers
55
views
java.lang.ArrayIndexOutOfBoundsException: Index 86 out of bounds for length 86
I use the next versions:
gatk 4.4.0.0
minimap2 2.26-r1175
samtools 1.19
I have a fastq file. And try to implement gatk MergeBamAlignment to generate a new ...
- 41
1
vote
1
answer
143
views
How to remove third codon positions from a charset in iqtree?
I need to build a phylogenetic tree using IQ-TREE, starting from a sequence alignment in CODON format of several invertebrate mitochondrial genes. These are my charsets:
...
