All Questions
Tagged with phylip or phylogenetics
152 questions with no upvoted or accepted answers
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How can I interpret multiple alignment results?
I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW and TCOFFEE.
I would like to ask if consistency score plays any role in the interpretation?
I ...
- 121
1
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153
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Problem with classification model of genomic data: every machine learing model predicts wrongly almost always the same subset of dataset
First of all, I'd like to apologize for any spelling or grammar mistakes.
I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
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68
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Unmapping Alternative reads in BAM file
I want to do some HLA typing, most of the tools require the bam file is aligned to primary genome without alternative read handling. From the International Genome Sample Resource project, I can get ...
- 121
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26
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What are the meanings of these transcript ids?
I have three types of transcripts for Rosa chinensis "Old Blush" homozygous genome v2.0 from GDR genome browser.
...
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How can I find genes of fundamental metabolic processes for an organism?
I want to find genes of fundamental metabolic processes in the Phytophthora cinnamomi genome. I'm using the genome sequence deposited in the NCBI and I'm searching ORF by ORF, using the ORF finder (...
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37
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Algorithmic Information Measurement of Human Genome Databases?
What is the highest data compression ratio achieved on a population of genomes measured to include the compressing algorithm itself? The size of the compressed database approximates its algorithmic ...
- 111
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54
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How can I get the estimate of lmFit function form limma package
This is the first time that I used lmfit function from the limma package
I'm a little bit confused on how to interpret the result.
is there a way to get the ...
- 21
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322
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Calculating the trimming parameter when constructing an additive phylogeny
How do you calculate the trimming parameter when constructing an additive phylogeny?
I think it has a relationship with the length of the shortest hanging edge, but I can't figure out how this works.
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67
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How to get a tabular summary from srspair alignment file?
I checked EMBOSS but there is no tabular output for pairwise alignment.
I can write a script but would like to know if there is already a tool to summarize an alignment in srspair format in the form ...
- 273
1
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152
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How can extract the list of genes name from the raw data in GEO?
The format of the raw data that upload in GEO is different, like TXT, CEL or other form. How can I extract the list of genes name from these formats? And then how can I normalize them with R?
I would ...
- 29
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23
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the positions computed by ms
I am doing simulations using a program 'ms':
https://snoweye.github.io/phyclust/document/msdoc.pdf
If you look at page 3 of this pdf, it explains the output produced by ms. The line which starts ...
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185
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Geneland R + Fortran error?
I am helping an undergrad with their project and their thesis advisor has requested they use GENELAND for their analysis. I haven't worked on this sort of analysis, so all I have done is install it in ...
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601
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Aligning nucleotide sequences in APE software
I am very new to APE software. I am trying to align complementary oligo-DNA strands using APE on macOS. I have both the forward and reverse sequence of an oligo-DNA insert in two separate files. But I ...
- 141
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18
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Finding the conserved region of protein in a given set of Kingdom
We have to find the conserved region of proteins in a given set of kingdom and we have to give more weightage to distantly related organism. What approach I should take to solve this problem?
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691
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How to create a dendrogram of clusters and reconstruct phylogenetic relationship
I'm working with a Daphnia data set looking at the 16s gene pulled from the BOLD database. So far I did
a multiple sequence alignment and
attempted to cluster and plot a dendrogram:
...
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40
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Stand alone chaining tool for existing blast hits?
I have a table of blast hits in a database that I'd like to chain. What is a good choice for a 'stand alone' chaining tool? Is it simple to implement in Perl, for example?
Example 'hit' data is here. ...
- 612
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990
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How to make year scale bar unit in figtree software?
I have generated phylogenetic trees for virus sequences by using beast software.
I observed in various research articles that the phylogentic trees also have a scale-bar (which mostly represents ...
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54
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How can I determine a mean sequence divergence for 10k sequences?
I am trying to analyze a number of repetitive sequences and as one step want to calculate a sequence divergence between the elements I found.
Now in theory I wanted to generate a MSA of the sequences ...
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123
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Mugsy error: Can't find species II dna at output/software/mugsy_x86-64-v1r2.3/mugsy line 501
I have installed mugsy in order to create a multiple genome alignment and a phylogenetic tree of several species of nematodes. The following command successfully pulls out the help:
...
- 2,479
1
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214
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igv_plotter error: Xvfb did not start
I am trying to get screenshots from alignments of reads to a genome in IGV (Integrated Genome Viewer) using igv_plotter.
...
- 2,479
1
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186
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Can Mauve export indels or is there an whole-genome aligner that can export indels?
I have aligned two whole genomes of the same species in Mauve using progressiveMauve. One of the genomes is 2 megabases longer than the other so I know it must contain some insertions. Looking at the ...
- 2,479
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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 ...
- 1
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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 ...
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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
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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 ...
- 59
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101
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Relationship between molecular weight and linear peptide
Sorry for this very beginner homework question:
Which of the following linear peptides is consistent with Spectrum = {0 71 99 101 103 128 129 199 200 204 227 230 231 298 303 328 330 332 333}? (Select ...
- 141
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27
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How to identify most important Amino Acid residues in a given protein?
Continuing from the title, in my context, important means that changing the set of AAs (either or one more many) changes the domain and/or fold and/or function and/or family etc.
I noticed that there ...
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211
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Extract SNPs from multiple sequence alignment
I’m wondering if folks have recommendations for tools/scripts to extract SNP sites from a multiple sequence alignment of consensus bacterial genomes? Specifically, I am interested in a multiple ...
- 111
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54
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What is the best tools to find all the somatic mutations?
I am a beginner in this field. I would like to know which is the best way to get all the mutations from a certain sample. At this point, I am considering using GATK (here) and Maftools (here). I don't ...
- 145
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100
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Help me to calculate Heaps Alpha value from the roary pangenome pipeline result?
I need to know whether my pan-genome is open or closed. For that, I need to calculate the ...
- 109
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45
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Are there different PAM matrices for different protein families? - How is the inferred common ancestor known to start with?
I am confused about the sequences one starts with to generate the PAM matrices.
The sequences to start with are supposed to diverge by no more than 1% (in sequence identity) wrt a common "...
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22
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Generating intercalation site in DNA for custom sequence
Thank you for your help.
Can anybody please tell me how I can generate an intercalation site in DNA at the base pairs I am interested on. I appreciate if you can please guide me to any tutorials or ...
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16
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xtract from eutilities not exctracting the information I need
I'm running the following command which uses the NCBI e-utilities:
esearch -db bioproject -query "PRJNA198476 [PRJA]" | esummary
This returns:
...
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36
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Drug-DNA complex simulation using AMBER
I want to carry out the simulation of drug-dna complex by placing the drug molecule at particular site in my DNA sequence (intercalating site). I have PDB files of both drug and DNA sequence. I will ...
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126
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Linking UK biobank patient IDs with their corresponding genetic data
I am analyzing ukbb data and I have patient IDs for both cases and controls. Now I want the genetic data of all patients based on their IDs.
I am trying to test with chromosome 5 as I have both bgen ...
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511
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pysam "Exec format" error
I am a beginner and trying to read a bam file in Python.
The lines below throw the error
...
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42
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Does the alignment need to be redone when using SAW method to test long branch attraction?
I am looking into different methods to test the long-branch attraction problem. In this chapter they talk about the SAW method - excluding one and the other taxa from the dataset and see if they ...
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114
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How likely is it to find primers sequences in already-trimmed reads?
So, I am analysing 18S amplicon data (fastq files) to be able to eventually investigate the taxa composition.
After removing primers (using cutadapt) from both R1 ...
- 348
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16
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How to run a phylogenetic analysis with non-independent data?
These are the facts: I am working with some morphological features. Each trait can have one of the following three states: 0, 1, 2.
State 0 is always independent.
But if there is a trait with state 1, ...
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41
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Is SNPRelate the goto package for PCA of SNP data in R?
I'm trying to evaluate a method that I'm not familiar with. They used SNPRelate. I'm wondering if this is the best / only choice... what other tools would you recommend?
Many thanks,
- 480
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53
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How is the instantaneous rate of an instantaneous rate matrix determined?
In molecular evolution, I know that the instantaneous rate of the rate matrix is the limit of the rate as time approaches 0, but what I don't understand is how this rate is established or what I can ...
- 317
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140
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Mrbayes stop at certain generation without error
I am using Mrbayes v 3.2.7 MPI version to infer phylogeny, and I set the ngeneration to 10,000,000, but it often stop at certain generation (usually far smaller than given generations). Even if I ...
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27
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Trouble aligning next generation sequencing data to reference genomes using QuasR package in Bioconductor. Cannot import .txt
I'm trying to check the quality of my paired end read sequencing data. I am following this pipeline (https://f1000research.com/articles/4-1062#ref-21) which uses QuasR in the first step.
My list of ...
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32
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DNA sequence error annotation
Suppose I generate a DNA sequence of the following pattern.
AAGTC
And after being passed through a channel with insertion, deletion and substitution errors obtain the following sequence
AAAGGC
Where ...
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59
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Best way to align to find inserted sequence
We have some RNA from knock-in mice, there are two different sequences we're looking for. We have aligned to the mouse genome using STAR but the sequence isn't there which isn't too surprising What is ...
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40
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Please help me with my command!
I am looking for a command to count the total number of unique proteins in a file. For instance I wrote a command to BLAST XYZ proteins as query against the DLY proteins as a database to determine the ...
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175
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workaround for error: Bad CPU type in executable c
I use clustal() from library ape every now and then, but now it doesnt work...
code:
sylvia.clus = clustal(sylvia.seq)
Error:
...
- 123
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144
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Greedy Motif Search [ Reasoning ]
I was able to execute the algorithm correctly. But I'm still trying to get a hold of the result I'm achieving.
This is the algorithm I'm trying to understand -
http://rosalind.info/problems/ba2d/
If ...
- 101
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48
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Coding vs non-coding DNA length
I am trying to calculate the total exonic length (in bp) in order to see where the coding-noncoding ratio of roughly 1% to 99% comes from.
We know all chromosomes total about 3 billion base pairs. So ...
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238
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Calculate Entropy for DNA Multiple Sequence Alignment in R
I am pretty new to R. So I apologize for asking maybe a very basic question.
Let's say I have a fasta file with sequence below:
...
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