From 3ab1f29e9dcb2090d11cdfae6df24b04c21ee499 Mon Sep 17 00:00:00 2001
From: "Workum, Dirk-Jan van" <dirk-jan.vanworkum@wur.nl>
Date: Fri, 18 Feb 2022 13:27:46 +0000
Subject: [PATCH] Hotfix msa protein alignment trees
---
.../bif/pantools/pangenome/MultipleSequenceAlignment.java | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java b/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java
index 2addc4140..95c5984cd 100644
--- a/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java
+++ b/src/main/java/nl/wur/bif/pantools/pangenome/MultipleSequenceAlignment.java
@@ -1624,9 +1624,12 @@ public class MultipleSequenceAlignment {
String path = outDirMsa + groupId + "/";
String inPath = path + "input/";
String outPath = path + "output/";
- if (alignNucleotide) { //
+ if (alignNucleotide) {
includeGenomeNumberInFasttree(inPath + "genome_order.info", outPath + "nuc" + dot + "newick");
}
+ if (alignProtein) {
+ includeGenomeNumberInFasttree(inPath + "genome_order.info", outPath + "prot" + dot + "newick");
+ }
}
}
--
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