All Questions
Tagged with phylip or phylogenetics
925 questions
4
votes
2
answers
196
views
BioPython bootstrap is not reliable?
Here i will show you a minimal working example of code and as you can see the support values for the tree is always 100.
I am using synthetic sequences of 100bp for 6 elements. The sequences have been ...
- 317
1
vote
0
answers
202
views
bwa mem hangs after a few thousand reads
I am trying to align a bunch of paired sample fastq files using bwa mem.
My original command was:
...
- 19
1
vote
1
answer
47
views
What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?
This question was also asked on reddit
Tries are a data structure that can be used to efficiently store and search for strings.
Tries created from an ordered sequence of strings differ from the ...
- 111
3
votes
2
answers
87
views
Sequence Alignment for sequences with the same length
I am doing research on a new method of optimizing sequence alignment process (Needleman - Wunsch algorithm) but the idea would only work with sequences that have the same length. I am wondering if ...
- 31
3
votes
2
answers
94
views
What is the best Query to retrieve DNA from NCBI?
I want to retrieve a sequence for many species from the Nucleotide database in NCBI.
I'm using a command line approach and I have to figure out what is the best query that will return exclusively the ...
- 317
1
vote
1
answer
33
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Annotation result for phylogenetic analysis shows no common evolutionary gene in contigs, can i change the contigs?
I'm currently doing my thesis with the topic of phylogenetic analysis and is taking references from the previous person in my university (who have done the same topics but different species).
They ...
- 11
1
vote
1
answer
56
views
What happened to the PhyLoTA browser?
A paper I'm reading from 2021[1] mentions doing some analysis on data from the PhyLoTA database, with this reference citation:
M. J. Sanderson et. al. 2008 The PhyLoTa Browser: processing GenBank for ...
- 216
4
votes
2
answers
276
views
How to create a phylogenetic tree from diverse mitochondrial genomes
I would like to create a phylogenetic tree for the most species in my dataset.
I'm starting with around 1200 species, but since it's not good practice to align short and long sequences I tried ...
- 317
3
votes
2
answers
149
views
Cannot obtain alignment summary after running Bowtie2
I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I obtain after finishing running the alignment is the following:
...
3
votes
1
answer
101
views
How can I export a pruned phylogenetic tree in nexus format in R?
I have a phylogenetic tree with a lot of different populations and I wanted to removes most of them and apply new names to the labels. I wrote this code:
...
- 329
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
1
answer
42
views
Find protein in DNA sequences with arbitrary encoding and possible frameshifts
I have a dataset with lots of DNA sequences (~10 M seqs, each ~6 KBp long).
I want to detect presence of a fixed given protein (~600 Bp / 200 aa) within each sequence and, if detected, obtain the ...
- 123
1
vote
1
answer
99
views
Approach for alignment-free phylogenetic tree generation using kmers
I have a general question about building phylogenetic trees without alignment:
I want to build a tree using an alignment-free approach by counting kmers. I have found a lot of information in the ...
- 1,063
2
votes
1
answer
38
views
What does the different sequences represent?
I am using this package nsdpy to download genome sequences from NCBI nucleotide database.
Specifically I am interested in the whole mitochondrial genome of different species, here I will use a subset ...
- 317
1
vote
1
answer
101
views
Is 16S sequencing cheaper than whole-genome sequencing for taxonomic assignment?
This is adapted from a question posted on reddit
In my work, I occasionally get asked about metagenomic sequencing, which (after further questioning) I discover means that the person wants to work out ...
- 15.1k
3
votes
1
answer
361
views
How can I convert my tree to the correct nexus format?
I would like to use the program BayesTraitV4. I have my phylogenetic tree in NEXUS format but the program does not accept it. I checked the example data and while they are also in NEXUS format, they ...
- 329
1
vote
0
answers
65
views
SNP How to detect regions of erratic pairwise alignment?
I have clusters of DNA sequences that contain some mutations. All the sequences in a cluster should contain the same mutations.
As the mutations aren't known, those clusters of sequences were pairwise-...
- 181
2
votes
1
answer
62
views
Compare substitution matrices
I am looking for methods to compare substitution matrices to determine which one is better for a given set of data / type of protein.
Do you know such methods / tools?
e.g. BLOSUM62 vs PHAT for 50k - ...
- 247
0
votes
1
answer
174
views
Mapping List of Probes/Primers/Short Oligos to a Reference Fasta/q
Could you help me bioinformatics SE people.
So I have been duckduckgo-ing up a storm and even consulted the AI overlords and haven't come up with a solid way to do this, but it is so fundamental to ...
- 51
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
1
vote
1
answer
69
views
Using average of sequence similarities when delimiting genera - how to deal with outliers?
Sometimes I am trying to see where a (bacterial) genus ends and where another one begins based on 16S rRNA phylogenies. Of course, the length and support of the branch matter a lot, but this question ...
- 1,027
1
vote
1
answer
95
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Genetic relationships between Cyanobacteria: terrestrial vs aquatic
I believe one of the site members is an expert in Cyanobacteria hence the question.
I'm looking for a comprehensive 'phylogenetic tree' of the phylum Cyanobacteria and want to identify all the ...
M__♦
- 13k
1
vote
1
answer
118
views
Scale on the y-axis in a tree rotated with 'layout_dendrogram()' using ggtree
I'm editing a time-scaled tree using ggtree. The dates are correctly adjusted when I apply the 'mrsd' command and 'theme_tree2()', but when I try to rotate the tree with 'layout_dendrogram()', the ...
1
vote
1
answer
65
views
phytools add.species.to.genus could not match your species to a genus
I have a species tree to which I am trying to add species, which includes a tip "Geissospermum laeve". When I run:
...
- 115
1
vote
1
answer
49
views
Finding linkage disequilibrium when I have a kinship matrix but not pedigree
I have a bunch of samples of a non-model organism divided in two groups: parental generation and offspring. I do not have a pedigree so I do not actually know who is a parent of who, and which are the ...
- 111
2
votes
1
answer
301
views
Correlation heatmap of RNA-seq clusters all samples together leading to very low no. of DEGs
I am writing to you to take an input or may be you can provide a different perspective. I am at wits end :(
So I have nearly 200 samples. These are separated into two groups (group I treated with ...
- 237
1
vote
1
answer
71
views
Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average
I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine... except some of the codon ...
- 217
2
votes
1
answer
83
views
How to determine the phylogeny of a specific set of genes
My goal is to understand the phylogeny of genes involved in bacterial restriction-modification systems, in psychrophilic bacteria.
To do so here is what I have done.
Downloaded the protein sequences ...
- 163
0
votes
1
answer
246
views
How to parallelize BEAST
I'm running BEAST v1.10.4 with BEAGLE v4.0.0. My dataset has one large partition and I have access to a machine with many CPUs so I would like to optimize performance by parallelizing the process. ...
- 111
1
vote
0
answers
259
views
Pacbio HIFI pbmm2 alignment metrics
I am new to pacbio sequencing data. I just did some alignment of pacbio HiFI data using pbmm2. I have the bam now, I would like to collect some metrics on the alignment. I used to work on the illumina ...
- 137
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
1
vote
1
answer
507
views
How to add bootstrap values to the phylogenetic tree generated by OrthoFinder?
When we run the OrthoFinder analysis tool on a group of genomes to get the orthologues shared by them one of the output files include a folder named 'Species_Tree' that contains a text file named '...
- 149
1
vote
1
answer
125
views
Evolutionary tree from SNP data
I would like to make an evolutionary tree using the SNP data from DArTseq. Are there any software or packages available for this purpose? I came across the software SNphylo, but its home page is not ...
- 11
1
vote
1
answer
211
views
How to use Gblocks for trimming single-copy gene sequences?
I have run OrthoFinder on a set of 11 genomes and got the results in a folder. From the output folder, I saved all the single-copy gene sequences in a single FASTA file and now wish to remove all gaps ...
- 149
4
votes
1
answer
342
views
How to get a GISAID account? I registered months ago, still no reply!
Inspired by amateur variant hunters, I would like to join the Pango lineage proposal community and help contribute to variant surveillance.
However, I cannot seem to get access to GISAID, the platform ...
- 43
0
votes
1
answer
475
views
Refactoring pandas using an iterator via chunksize
This question was also asked on Stack Overflow
Bioinformatics rationale eggNOG files can be very big and sump all available RAM for regular to medium sized desktops.
I am looking for advice on using ...
M__♦
- 13k
2
votes
1
answer
44
views
NCBI Blast databases - cannot find some databases
I'm working with a system that does local BLAST searches using some preconfigured BLAST databases. From what I see, these were updated within the last year, but I cannot find any current databases ...
- 175
0
votes
1
answer
330
views
Blast output file only shows 500 lines -outfmt 6
I had created databases of different sets of metagenome datasets - one with 6 runs, other with 48 runs, another with 100 runs, etc using the accession list for each of these datasets and makeblastdb ...
- 149
1
vote
0
answers
208
views
Mapping statistics from the bam files
I would like to find the mapping statistics from the sorted bam files.
Samtools flagstat gives the output only for a single file. What is the easiest way to find the mapping statistics for all ...
- 11
1
vote
0
answers
95
views
How to identify all descendents of a branch on a phylogeny
I'm trying to simulate the evolution of binary traits on phylogenies in R to end up with a dataset of the traits held by each tip. Starting at the root, at every timestep, new traits are added with a ...
3
votes
1
answer
112
views
What is the limit of partition incompleteness in Bayesian MCMC?
I am seeking advice on whether or not to incorporate incomplete data into my BEAST analysis.
I have HIV data consisting of two partitions of the pol gene: one that is 1.2 kb in length and present in ...
- 435
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
3
votes
1
answer
71
views
compare fasta sequences in pairs and collect metrics
I have 96 fasta files (A1, A2, A3...) from one plasmid assembly pipeline, and I have another 96 fasta files (B1, B2, B3 ...) from another plasmid assembly pipeline.
I would like to compare pair ...
- 137
2
votes
2
answers
72
views
RNAseq alignment: best practices for aligning to multiple isoforms?
I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed genes between experimental conditions.
Many of my (de novo assembled and ...
- 23
2
votes
1
answer
88
views
Using ticks on the x axis or a scale bar when visualisizing a phylogram?
When visuliazing a phylogram is it preferable to show ticks on the x axis or a scale bar?
Given an example tree with branch lengths in newick format ...
- 73
0
votes
1
answer
157
views
Is my reference sequence too small?
I'm trying to map ONT long reads to a portion of a gene I'm looking at. The region is about 25bp long. When I search for the region in the document it pulls up the sequence in every read but when I ...
- 1,063
3
votes
1
answer
304
views
Plot phylogenetic tree from list of edges
I have a dataset that I wish to convert to tree or phylo format like in the ape package, in order to plot the phylogenetic tree. It is formatted like a list of ...
- 33
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
1
vote
0
answers
85
views
eggNOG API, how's it work?
Background eggNOG uses seed orthologues which correspond to its own internal database, so for example J421_1876 can be placed in its online search engine here. This ...
M__♦
- 13k
3
votes
1
answer
107
views
Sanger Sequencing Knitting Error
I am doing a project where I am reproducing the analysis from the article "sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R". Below is the example chunk for ...
- 31