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Thanks for the suggestion. Yep, the only way to get something from it was parsing it along. It's like a pre-clustal aligment with extra headers (it is from mid-late 90's). -
I suggest writing a PERL script to convert the data into the format you desire.
The alignment file looks very similar to Phylip format. Maybe you can just load it into Excel and manually modify it to the desired format.Leave a comment:
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What file format is this?
Hi everyone,
I found this alignment in a format I don't recognize, neither my phylogenetic programs. Any idea? And any way to convert it to fasta, phylip, etc...
Thanks
Code:193 Ce 13A10 Z46934 -------------------------MTQSLAHKNAWQC-- 13 194 Ce 13A8 Z48717 T10B9.4 ---------------------------------------- 0 195 Ce 13A7 Z48717 T10B9.10-------------------------MSFSI---------- 5 196 Ce 13A6 Z48717 T10B9.3 -------------------------MIFVL---------- 5 197 Ce 13A5 Z48717 T10B9.2 -------------------------MSLSI---------- 5 198 Ce 13A4 Z48717 T10B9.1 -------------------------MSLSL---------- 5 199 Ce 13A3 Z48717 T10B9.5 -------------------------MSLSI---------- 5 200 Ce 13A2 Z48717 T10B9.7 -------------------------MSLGF---------- 5 201 Ce 13A1 Z48717 T10B9.8 -------------------------MGYF----------- 4 202 Ce 25A1 Z66495 C36A4.1 -------------------------MAL------------ 0 203 Ce 25A2 Z66495 C36A4.2 -------------------------MAL------------ 0 204 Ce 25A3 Z66495 C36A4.3 -------------------------MAF------------ 0 205 Ce 25A4 Z66495 C36A4.6 -------------------------MAI------------ 0 206 Ce 14A1 Z50742 K09A11.2---------------------------------------- 0 207 Ce 14A2 Z50742 K09A11.3---------------------------------------- 0 208 Ce 14A3 Z50742 K09A11.4---------------------------------------- 0 209 Ce 14A4 Z50742 + R04D3 ---------------------------------------- 0 210 Ce 16A1 Z54269 ---------------------------------------- 0 Ce U55365 C12D5.7 ---------------------------------------- 0 Ce U50311 C25E10.2---------------------------------------- 0 211 Ce 22A1 U39648 T13C5.1 SSWIKCRDWMAFALSHHIIMGIYLLILRNFLPQVVPDFEW 0 212 Ce 23A1 U39472 B0304.3 -------------MPIAYFLPSQVNSGVCCLICRHWYLIG 0
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Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis
After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...05-23-2023, 12:26 PM -
Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.
Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...05-19-2023, 10:03 AM -
With new tools and computational resources being released regularly, it can be hard to determine which are best suited for the analysis process and which older tools continue to be maintained. In an effort to assist the sequencing community, we interviewed three highly skilled bioinformaticians about their recommended tools for several important analysis applications.
Quality control and preprocessing tools
“Garbage in, garbage out” is a popular...05-16-2023, 10:11 AM
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