Running Multiple Alignments in MEGA with a script produces errors. · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Running Multiple Alignments in MEGA with a script produces errors.

I need to run about 100 fasta files through MEGA v7 for multiple alignments. I have tried writing scripts and using command line (in both Linux and Windows) to run alignments using the .mao settings file, but each time after completion, MEGA throws an error, saying there is an invalid character "_" in some line of the file. However, alignments run fine with the Windows GUI version. Does anyone know how to get around this error?

next-gen rna-seq mega multiple-alignment

• 3,111 views • link

updated 3.2 years ago by Ram

• written 10.4 years ago by rachelrodgers12 •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Problem running DeepTMHMM with Docker
written 2.5 years ago by Elizabeth •

Hello All, I'm attempting to run DeepTMHMM on Docker. Due to the size of my fasta file, I prefer running it locally rather than using …
Bioinformatics package
written 3.4 years ago by zainabi8077 •

I'm attempting to create a python GUI for analysing tRNA-Seq data that can run on Linux and Windows. It is necessary to run several applications, …
Filtlong and Flye
written 3.8 years ago by awhale01 •

Hi, I am trying to run Flye on some filtered Fastq files of ONT reads. I am using Filtlong for some light QC before running …
prinseq error: Use of uninitialized value $qual in scalar chomp
written 8.2 years ago by mforthman •

Running fastq-generated SRA files from NCBI through prinseq-lite. The program generates an error: Use of uninitialized value $qual in scalar chomp at /apps/prinseq/0.20.4/bin/prinseq-lite.pl line 2583, …
A question about Perl symbol lookup error
written 9.0 years ago by nancydong20

Hello everyone! I installed several Perl modules in a local library on a cluster, since I don't have root access. After this, even though the …
Errors when re-importing an alignment back to Mega
written 9.4 years ago by genya35 •

Hello, I would really appreciate if someone could advise on the following error with Mega7 GUI version. I'm experiencing errors when trying to re-import alignments …
Error in Geneland
written 9.7 years ago by oklagirl •

Hello, I have used Geneland in R in the past with no issues. I am working on a SNP dataset of approximately 35,353 SNPs. I …
GSEA Error Message - "Dataset not set"
written 11.9 years ago by aditi.qamra

Hi, I am trying to run GSEA or the first time using the GUI application. I created all files in the formats specified and they …
PLINK ERROR: ERROR: --ld-snp {marker} not found
written 12.3 years ago by Aishwarya Kulkarni

Hi I am passing a SNP through a variable and the step reads the SNP from the variable correctly since in the log it displays: …
Mauve Contig Mover
written 13.1 years ago by HG

<p>Dear all, Currently i am using "Mauve contig mover" to make an ordering of contig. I have one contig file (around 200 contig) and one …