All Questions
Tagged with phylip or phylogenetics
925 questions
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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 ...
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0
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1
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20
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retrieving divergent regions of a pairwise alignment
I am relatively new here. I am looking for a tool that can retrieve all divergent regions between two strains of E.coli into a different file. I also wanted to be sure that using global alignment ...
0
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1
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21
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Phylogenetic Separation
I am having a bothersome issue with my current approach in generating a phylogenetic tree of yeast samples, where samples from two groups (in-house and public NCBI data) form separate clades, despite ...
- 1,063
2
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1
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31
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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 ...
1
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1
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56
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How can I normalize DNAseq nanopore metagenomics data?
I'm working on antimicrobial resistance (AMR) surveillance in treated water samples using nanopore long-read DNA sequencing analysis. After analyzing my data with the KMA tool (a k-mer read alignment ...
- 155
1
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1
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36
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Normalization and Comparison of AMR Gene Tables from Long-Read Metagenomics Data without Spike-In Controls
I am conducting antimicrobial resistance (AMR) surveillance in water samples using long-read metagenomics (Nanopore sequencing). After analyzing the data with KMA (a k-mer read alignment tool, Clausen ...
- 155
2
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0
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21
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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
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1
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41
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Difference between FASTA/FASTQ formats and Plink2 PACKEDPED format
I'm new to bioinformatics, and in my first experiments I've always used FASTA/FASTQ files for my analysis. What I read is that in general terms FASTQs are used for reads and FASTAs for reference ...
- 151
2
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2
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71
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What is the the principle and mechanism of k-mer alignment?
I'm currently exploring the concept of k-mer alignment in bioinformatics and came across some information suggesting that the k-mer approach is considered a non-alignment method. Could someone clarify ...
- 155
0
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1
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22
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Identifying Accurate Exon Boundaries for Highly Polymorphic Exon 2 in MHC Class II Beta Gene
I am working on annotating the MHC class II beta gene in a bird species and need some assistance in determining the correct splice sites for exon 2. The sequences I obtained seem to work with multiple ...
user21035
1
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1
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22
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What is the Impact of Adjusting the -reward Parameter in KMA Aligner?
I am currently utilizing the KMA aligner developed by Clausen et al., as detailed in their BMC Bioinformatics article (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2336-6). ...
- 155
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1
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53
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Understanding the Relationship Between ConClave Score, Depth, and Template Length in KMA Aligner Results
I am currently analyzing my nanopore metagenomic sequencing data. After demultiplexing and trimming, I am using the KMA (k-mer alignment) aligner by Clausen et al. (https://bmcbioinformatics....
- 155
1
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1
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16
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How can I include the start and end sequence number while doing MSA alignment with any alignment tool like CLUSTALW?
I have this assignment to align sequences from the domains of 5 different proteins. I extracted the domain sequences. I have done the alignment, but I realize I need to number each sequence (since ...
- 23
1
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2
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104
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How to align two FASTAs and extract the aligned part?
I have two fastas and I'd like to align them to extract the aligned part. I've just found examples (Several of them) of alignment of FASTQs using FASTA references, so I'm not sure if what I want ...
- 151
1
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1
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21
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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
4
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1
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85
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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
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1
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37
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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
1
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0
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29
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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
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0
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40
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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
3
votes
1
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54
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Passing data from the Agilent Trimmer utility to bwa-mem2 via a named pipe
I am trying to use a named pipe to pass data from the Trimmer utility from the AGeNT toolbox from Agilent, through bwa-mem2. The normal behavior is that the Trimmer utility writes trimmed fastq files ...
1
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1
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27
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Where to obtain fastq_illumina_filter
I'm setting up a snakemake pipeline for my lab, and I'd like to install fastq_illumina_filter. All links I can find point to this address for info on it, but the website seems to be down.
Is there ...
- 412
2
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1
answer
65
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Creating a Multiple Sequence Alignment From Eggnog Mapper Results
I used Eggnog mapper to annotate several rockfish genomes and the output files have qstart and qend values for each gene.
I plan to use the phylogenetic trees for a few different genes for positive ...
- 23
3
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2
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97
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Biopython / ETE3 get subtree of a newick tree
I can not find a good example how to extract a subtree from a phylogenetic tree with either library.
I can load newick files etc, but not sure how to search for a ...
- 195
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30
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0
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1
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38
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How can I Find DNA sequence of promoter region of a gene?
I have a fungal sequence from Candida albicans, sequenced via Sanger sequencing, that I want to check for quality and contamination.
I have 2 questions:
Could I use Alignment ? or BLAST or ...
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1
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0
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37
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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
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1
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58
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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
2
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1
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140
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Aligning FASTQs to FASTA reference
I'd like to align some FASTQs to an average mtDNA FASTA file that I have downloaded so I can have the human mtDNA isolated from those FASTQs. For that, I used bowtie2. Can I expect that after running ...
- 151
2
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0
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45
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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
1
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2
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74
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How to download the same 18S rRNA gene region for multiple species?
I need 18S rRNA gene sequences for a wide variety of eukaryotic species.
I know that Ensembl has this gene sequence, but I don't understand what is the correct protocol to download the sequences. I ...
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2
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1
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34
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Why is my phylogenetic tree always splitting into one leaf and one node?
I used RAxML software on about 300 species mtDNA region (COI gene).
Unfortunately I used a highly variable region so my tree only has highly support values for branches close to the leaves.
But I also ...
- 33
4
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1
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27
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How to interpret high support values for terminal nodes and low for more ancient nodes?
I made a phylogenetic tree for about 300 species using a region of the COX1 gene. The tree looks visually meaningful: species of the same genus are all clustered together.
Then I performed a 350-...
- 317
1
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1
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188
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All against all sequence alignment
I have a large set of protein sequences and would like to create a "similarity matrix" out of them (for phylo trees later). So I have to run n(n-1) ...
- 195
3
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1
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48
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How many ML tree should I build?
I created a phylogenetic tree of 328 species using RAxML. I run the ML algorithm 20 times and I chose the best tree (the one with the highest likelihood).
The choice of 20 iterations was based on a ...
- 317
1
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0
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25
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Biopython PhyloTree to PyVis Network
We are trying to convert a Phylogenetic tree to networkx previously calculated with
...
- 195
1
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2
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97
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How to know if FASTQ/BAM is from reference genome (FASTA)?
I'm new to bioinformatics. I have a problem in which I have a FASTA reference genome and lots of reads in FASTQ files. Some of them could be contaminants, so I'd like to filter them out and get only ...
- 151
2
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1
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55
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Salmon Multiple File SCRIPT giving error
Hi I am using Salmon quantitation for multiple fastq paired files using following code
...
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4
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1
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109
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split fastq file containing a sequence block at different locations
I have some fastq files (obtained from nanopore sequencing) that contain reads that can be of either of these 5 forms:
a known CDS with 3'UTR:
...
4
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1
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69
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Finding homologous regions in multiple whole genomes
Right now I have six genomes that I want to compare and identify homologous regions in the genomes. I have run nucmer, show-coords and obtained the output files. An example is shown below with Genome ...
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0
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1
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69
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Defining out-groups in MEGA
I am using the MEGA software for trimming protein sequences and building phylogenetic trees.
How can I define out-groups of phylogenetic tree in MEGA? Is there a way to calculate the distances of each ...
6
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1
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92
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How many false positive duplicates are marked using just the position of first unclipped base?
In the popular picard MarkDuplicates tool, a read is marked as a duplicate if it has the same position as another read starting from their first unclipped base in ...
- 63
3
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2
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107
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What is the best way to acquire protein isoform sequence alignment?
[Update] Thanks @terdon. To clarify my question:
I have a bunch of protein isoforms sequences (produced by the transcripts in the figure) and I want to align protein products (e.g., proteins produced ...
- 31
4
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2
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114
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probability of finding a 5 amino acids in a row within a proteome
How to calculate the probability of finding two proteins that share a 5 amino acid long motif from a proteome of around 1067 proteins that have an average length of 65 residues.
The probability of a ...
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1
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0
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55
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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 ...
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1
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45
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tBLASTn vs NCBI TSA
Is there a way to blast my proteins against all the TSA (Transcriptome Shotgun Assembly Sequence Database) belonging to a specific taxonomy using command line?
Thanks,
Marco
- 161
2
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1
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112
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align to the whole hg38 genome, then split bam and collect metrics on each bam issue
I am doing some coverage analysis on deep sequencing human genome. I first align to the whole hg38 genome, then split bam to each chrom, and collect metrics on bam for each chom.
I first split using ...
- 137
5
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2
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300
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Why are Minimap2 alignments different with CIGAR generation flag?
I am using Minimap2 (v2.26-r1175) in Linux to generate a sequence alignment between the Streptomyces coelicolor A3(2) chromosome (ref.fa) and the Mycobacterium ...
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1
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1
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143
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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:
...
2
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0
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280
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Fst calculation from VCF files
I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and ...
- 21
0
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1
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142
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Aligning sequences with multiple genetic codes!
I am doing a project on duplicated genes and I have a major difficulty on how to align sequences that use different genetic codes. I work with fasta files that contain sequences of protein coding ...
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