add more help about formats

tools/quicktree/quicktree.xml

@@ -137,11 +137,39 @@ QuickTree accepts both distance matrix and multiple-sequence-aligment inputs. Th
 Alignments can be supplied in various other formats (fasta, phylip, clustalw, pfam, psiblast, selex) and will be converted to Stockholm format with the esl-reformat program,
 which is part of the HMMer package (hmmer.org).
 
+**Output**
 
+Quicktree will output either a distance matrix (in PHYLIP format, square distance matrix) or a Newick tree.
+
+
+**File Formats**
+
+The **distance matrix** input should be in phylip format, it can be a square matrix or a lower triangle matrix.
+The distance matrix output by quicktree will be a square matrix.
+
+Example square distance matrix in phylip format::
+
+       5
+    Alpha      0.000 1.000 2.000 3.000 3.000
+    Beta       1.000 0.000 2.000 3.000 3.000
+    Gamma      2.000 2.000 0.000 3.000 3.000
+    Delta      3.000 3.000 3.000 0.000 1.000
+    Epsilon    3.000 3.000 3.000 1.000 0.000
+
+Example of a lower triangle matrix::
+
+       7
+    Mouse
+    Bovine      1.7043
+    Lemur       2.0235  1.1901
+    Orang       2.0593  1.2005  1.5356
+    Gorilla     1.6664  1.3460  1.4577  1.5935
+    Chimp       1.7320  1.3757  1.7803  1.7119  1.0635
+    Human       1.7101  1.3956  1.6661  1.7599  1.0557  0.6933
 
-**Output**
 
-Quicktree will output either a distance matrix (in PHYLIP format) or a Newick tree.
+* For more details about the PHYLIP distance matrix format, see https://phylipweb.github.io/phylip/doc/distance.html
+* For more details about the Newick output format, see https://phylipweb.github.io/phylip/newicktree.html
 
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