updated all

_posts/2023-10-09-msa-phylogeny.md

@@ -0,0 +1,81 @@
+---
+layout: post
+title:  "MSA & Phylogeny"
+image: assets/images/wsl2.png
+---
+## Multiple Sequence Alignment (MSA)
+
+1. Open the MSA tool.
+2. Set the reference sequence to "AFUA_5G01230."
+3. Click on "Align > Edit or build alignment."
+4. Choose "Create a new alignment."
+5. Select "Protein" as the sequence type.
+6. Paste the first sequence (already copied from a fasta/text file) into "Sequence 1."
+7. Delete the placeholder "Sequence 1" entry.
+
+Now you have your data ready for alignment.
+
+8. Go to "Alignment > Align by Clustalw/ MUSCLE."
+9. If nothing is selected, choose "Select all" and click "Ok."
+10. Keep the alignment options as default and click "Ok."
+
+Wait for the alignment process to complete.
+
+11. Once alignment is complete, go to "Data > Export alignment > MEGA format."
+
+## MUSCLE: Default Parameters
+
+12. In the MUSCLE parameters window, you'll see the following default settings:
+
+   - **GAP penalties:**
+     - Gap open: -2.90
+     - Gap extend: 0.00
+     - Hydrophobicity multiplier: 1.20
+
+   - **Memory Iterations:**
+     - Max memory in MB: 2048
+     - Max iterations: 16
+
+   - **Advanced options:**
+     - Cluster method (iter 1,2): UPGMA
+     - Cluster method (iter): UPGMA
+     - Min diagonal length (lambda): 24
+
+13. Give a name for your alignment and save it, then close the window.
+
+## Phylogeny Reconstruction
+
+14. Navigate to "Phylogeny > Construct/Test-neighbor-joining Tree."
+15. When asked about the current data, select "No."
+16. When asked if you want to preserve data, select "No."
+17. It will ask if you want to save the alignment again, do so.
+
+It will open the last sequence alignment for phylogeny reconstruction.
+
+## Phylogeny Reconstruction Parameters
+
+18. In the "Phylogeny reconstruction parameters" window, configure the following settings:
+
+   - **ANALYSIS:**
+     - Scope: All selected taxa
+     - Statistical method: Neighbor-joining
+
+   - **PHYLOGENY TEST:**
+     - Test of phylogeny: Bootstrap method (You can choose the number of bootstrap replicates, e.g., 100 or 1000)
+
+   - **SUBSTITUTIONAL MODEL:**
+     - Substitution type: Amino acids
+     - Model/method: Jones-Taylor-Thornton (jTT) model
+
+   - **RATES AND PATTERNS:**
+     - Rates among sites: Uniform rates
+     - Pattern among lineages: Same (homogeneous)
+
+   - **DATA SUBSET TO USE:**
+     - Gaps/missing data treatment: Pairwise deletion
+     - Site coverage cutoff (%): Not applicable
+
+   - **SYSTEM RESOURCES USAGE:**
+     - NUMBER OF THREADS: 4
+
+19. After configuring these settings, proceed with the phylogeny reconstruction.