All output files will be placed in the directory specified with -o
GRAMPA creates three main output files and a filtered tree file (if necessary).
+GRAMPA creates four output files, a log file, and a filtered tree file (if necessary).
GRAMPA also creates a directory within the output directory called groups_dir. This just stores the gene tree groupings for each MUL-tree (in pickled format) so GRAMPA doesn't eat up a lot of RAM during reconciliations. This can be ignored/deleted
This is the main output file and contains some log info for the current run and it gives the total reconciliation score for each MUL-tree - considered. At the bottom of the file it will display the MUL-tree with the minimum reconciliation score.
- -# Tree # H1 node H2 node Tree string Total score
-ST (((a,(x,(y,z)<1>)<2>)<3>,b)<4>,(c,d)<5>)<6> 115
-MT-1 <2> a ((((a,(x*,(y*,z*)<1>)<2>)<3>,(x+,(y+,z+)<4>)<5>)<6>,b)<7>,(c,d)<8>)<9> 119
-MT-2 <2> c (((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,((c,(x*,(y*,z*)<5>)<6>)<7>,d)<8>)<9> 96
-MT-3 <2> b (((a,(x+,(y+,z+)<1>)<2>)<3>,(b,(x*,(y*,z*)<4>)<5>)<6>)<7>,(c,d)<8>)<9> 130
-MT-4 <2> d (((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(c,(d,(x*,(y*,z*)<5>)<6>)<7>)<8>)<9> 76
-MT-5 <2> <3> ((((a,(x+,(y+,z+)<1>)<2>)<3>,(x*,(y*,z*)<4>)<5>)<6>,b)<7>,(c,d)<8>)<9> 119
-MT-6 <2> <2> (((a,((x+,(y+,z+)<1>)<2>,(x*,(y*,z*)<3>)<4>)<5>)<6>,b)<7>,(c,d)<8>)<9> 145
-MT-7 <2> <6> ((((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(c,d)<5>)<6>,(x*,(y*,z*)<7>)<8>)<9> 132
-MT-8 <2> <4> ((((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(x*,(y*,z*)<5>)<6>)<7>,(c,d)<8>)<9> 118
-MT-9 <2> <5> (((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,((c,d)<5>,(x*,(y*,z*)<6>)<7>)<8>)<9> 95
-# ---------
-The MUL-tree with the minimum parsimony score is MT-4: (((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(c,(d,(x*,(y*,z*)<5>)<6>)<7>)<8>)<9>
-Score = 76
+ grampa-scores.txt
+ This is the main output file and contains the total reconciliation score for each MUL-tree considered, sorted in ascending order.
+
+
-
- - The first line has the headers for the columns of the output table. Note that H1 node and H2 node are always nodes in the singly
- labeled tree.
- - The total reconciliation score in the last column is the sum of all reconciliation scores for all gene trees for that MUL-tree.
-
-
+ The first line of this file contains the headers, defined as follows for each subsequent row:
+
+
+
+
+
+
+ mul.tree
+ h1.node
+ h2.node
+ score
+ mul.tree
+
+
+
+
+ The ID of the MUL-tree
+ The H1 node in the species tree for the current MUL-tree
+ The H2 node in the species tree for the current MUL-tree
+ The total parsimony score for the current MUL-tree
+ The Newick formatted tree string for the MUL-tree, with hybrid clades indicated with *
+
+
+
+
- grampa_det.txt
+
+ Please note that the input singly-labeled species tree always has the ID of 0
+
+
+ grampa-detailed.txt
The secondary output file contains detailed output describing the reconciliation scores from each gene tree to the lowest scoring MUL-tree.
-# MT-4:(((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(c,(d,(x*,(y*,z*)<5>)<6>)<7>)<8>)<9> H1 Node:<2> H2 Node:d
-# GT/MT combo # dups # losses Total score
-GT-1 to MT-4 1 1 2
-GT-2 to MT-4 1 2 3
-GT-3 to MT-4 1 3 4
-GT-4 to MT-4 1 2 3
-.
-.
-.
-GT-25 to MT-4 0 1 1
-# Gene trees with multiple maps: 1
-# Total parsimony score for MT-4: 76
+
- grampa_checknums.txt
+
+ The first line of this file contains the headers, defined as follows for each subsequent row:
+
+
+
+
+
+
+ mul.tree
+ gene.tree
+ dups
+ losses
+ total score
+
+
+
+
+ The ID of the MUL-tree
+ The ID of the gene tree being reconciled to the MUL-tree
+ The number of duplications on this gene tree given this MUL-tree
+ The number of losses on this gene tree given this MUL-tree
+ The sum of dups and losses for this gene tree and MUL-tree
+
+
+
+
+
+
+ Note that the lowest score for some GT/MT combos can have multiple maps. In these cases, we report all possible scores.
+
+
+ grampa-dup-counts.txt
+
+ For the 6 lowest scoring MUL-trees, GRAMPA counts the number of duplications along each branch in the MUL-tree summed
+ over all gene trees.
+
+
+
+ The first line of this file contains the headers, defined as follows for each subsequent row:
+
+
+
+
+
+
+ mul.tree
+ node
+ dups
+
+
+
+
+ The ID of the MUL-tree
+ The node ID for the current MUL-tree
+ The total number of duplications over all gene tres along the branch above the node in the MUL-tree
+
+
+
+
+
+ grampa-checknums.txt
GRAMPA must calculate how many combinations of maps there are for each gene-tree/MUL-tree pair and filter out those that are over
the group cap in any combo before any reconciliations can be done. This filtering ensures that all MUL-trees are reconciled to
the same set of gene-trees. The number of groups for each gene-tree/MUL-tree is recorded in this file.
-# GT/MT combo # Groups # Fixed # Combinations
-# MT-1:((((a,(x*,(y*,z*)<1>)<2>)<3>,(x+,(y+,z+)<4>)<5>)<6>,b)<7>,(c,d)<8>)<9> H1 Node:<2> H2 Node:a
-GT-1 to MT-1 2 0 4
-GT-2 to MT-1 1 1 2
-GT-3 to MT-1 1 1 2
-GT-4 to MT-1 1 1 2
-.
-.
-.
-GT-25 to MT-9 0 2 1
+
-
- - The first line in the file contains the table headers. For each MUL-tree there is also a line giving som info about it.
- - If a gene tree is over the cap specified with
-c X then the message Number of
- groups over group cap (-c set to X) -- Filtering. will also be displayed on the line.
-
-
+ The first line of this file contains the headers, defined as follows for each subsequent row:
+
+
+
+
+
+
+ mul.tree
+ gene.tree
+ groups
+ fixed
+ combinations
+ over.cap.filtered
+
+
+
+
+ The ID of the MUL-tree
+ The ID of the gene tree to be reconciled to the MUL-tree
+ The number of distinct hybrid clades in the gene tree
+ The number of hybrid clades in the gene tree that also group with a sister species from the singly-labeled tree
+ The total number of mappings to try for the gene tree with this MUL-tree
+ Either Y or N to indicate whether the number of groups exceeds the number set with -c
+
+
+
+
+
+ grampa-trees-filtered.txt
+
+ A text file with the gene trees used for this GRAMPA run, after filtering by the group cap. One tree per line.
+
+
+ grampa.log
+
+ A log file containing run time information and a summary of the lowest scoring MUL-tree.
+
-h1.
If nothing is entered all possible nodes for the current h1 will be considered.-s, -h1, and -h2.-s, -h1, and -h2 and write them to the log file.-h1 and -h2 are not speci
of H1 and H2!-c : The group cap-h1 and -h2 are not speci
(((a,(x,(y,z)<1>)<2>)<3>,b)<4>,(c,d)<5>)<6>--numtrees : Building MUL-trees+ This option quickly calculates how many MUL-trees are to be built with a given H1 and H2 set. If neither H1 or H2 are set + it will display the total number of MUL-trees possible for the input species tree. This information is printed to the screen. +
+--buildmultrees : Building MUL-treesThis option can be used with -s, -h1, and -h2 to build
@@ -440,6 +561,10 @@
-h1 and -h2 are not speci
Will yield the following output in the main output file (multree_ex/grampa_out.txt):
((((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(x*,(y*,z*)<5>)<6>)<7>,(c,d)<8>)<9>+ The MUL-trees are written to the log file. +
--checknums : Group counting-h1 and -h2 are not speci
best setting for -c.
+ --st-only : Group counting+ By default, GRAMPA reconciles the gene trees to all specified MUL-trees as well as the singly-labeled input species tree. Set this option to ONLY + do reconciliations to the singly-labeled input species tree. +
+--no-st : Group counting+ By default, GRAMPA reconciles the gene trees to all specified MUL-trees as well as the singly-labeled input species tree. Set this option to SKIP + reconciliations to the singly-labeled input species tree. +
+--maps : Output node mappingsSet this option to output the LCA node mappings along with the reconciliation scores to the detailed output file. This adds a column - to the _det.txt output file with that gene tree with the nodes re-labeled to include the maps, dups, and losses along that branch.
- -# GT/MT combo # dups # losses Total score Maps
-GT-1 to MT-4 1 1 2 (((1_a[a+-0],((1_x[x+-0],(1_y[y+-0],1_z[z+-0])<1>[<1>+-0])<2>[<2>+-0],(2_x[x+-0],(2_y[y+-0],2_z[z+-0])<3>[<1>+-0])<4>[<2>+-0])<5>[<2>+-1])<6>[<3>+-0],1_b[b+-0])<7>[<4>+-0],(1_c[c+-0],1_d[d+-0])<8>[<8>+-0])<9>[<9>+-0]
-GT-2 to MT-4 1 2 3 ((((1_a[a+-0],(1_x[x+-0],(1_y[y+-0],1_z[z+-0])<1>[<1>+-0])<2>[<2>+-0])<3>[<3>+-0],(2_x[x+-0],(2_y[y+-0],2_z[z+-0])<4>[<1>+-0])<5>[<2>+-0])<6>[<3>+-1],1_b[b+-0])<7>[<4>+-0],(1_c[c+-0],1_d[d+-0])<8>[<8>+-0])<9>[<9>+-0]
-GT-3 to MT-4 1 3 4 ((((1_a[a+-0],(1_x[x+-0],(1_y[y+-0],1_z[z+-0])<1>[<1>+-0])<2>[<2>+-0])<3>[<3>+-0],1_b[b+-0])<4>[<4>+-0],(2_x[x+-0],(2_y[y+-0],2_z[z+-0])<5>[<1>+-0])<6>[<2>+-0])<7>[<4>+-1],(1_c[c+-0],1_d[d+-0])<8>[<8>+-0])<9>[<9>+-0]
-GT-4 to MT-4 1 2 3 ((((1_a[a+-0],(2_x[x+-0],(2_y[y+-0],2_z[z+-0])<1>[<1>+-0])<2>[<2>+-0])<3>[<3>+-0],(1_x[x+-0],(1_y[y+-0],1_z[z+-0])<4>[<1>+-0])<5>[<2>+-0])<6>[<3>+-1],1_b[b+-0])<7>[<4>+-0],(1_c[c+-0],1_d[d+-0])<8>[<8>+-0])<9>[<9>+-0]
-
-.
-.
-.
-GT-25 to MT-4 0 1 1 (((1_a[a+-0],1_x[x+-0])<1>[<3>+-0],1_b[b+-0])<2>[<4>+-0],(1_c[c+-0],(1_d[d+-0],(2_x[x*-0],(1_y[y*-0],1_z[z*-0])<3>[<5>+-0])<4>[<6>+-0])<5>[<7>+-0])<6>[<8>+-0])<7>[<9>+-0]
-# Gene trees with multiple maps: 1
-# Total parsimony score for MT-4: 76
+
+ This option adds a column to the grampa-detailed.txt with the actual LCA node mappings for each gene tree and MUL-tree combo. The column
+ contains a Newick formatted version of the gene tree with nodes labeled as follows:
+
+
+ Node[Map-Dups]
+ Where Map indicates the node in the MUL-tree that this gene tree node maps to and Dups the number of duplications this mapping incurs. These trees
+ can be rendered with a tree viewer such as SeaView
+ or FigTree.
+
+
@@ -484,7 +627,7 @@ If -h1 and -h2 are not speci
diff --git a/docs/scripts/generators/readme_generator.py b/docs/scripts/generators/readme_generator.py
index b9f82b7..54649e6 100644
--- a/docs/scripts/generators/readme_generator.py
+++ b/docs/scripts/generators/readme_generator.py
@@ -4,8 +4,8 @@
############################################################
import sys, os
-sys.path.append('..')
-import lib.read_chunks as RC
+sys.path.append(os.path.abspath('../lib/'))
+import read_chunks as RC
######################
# HTML template
@@ -73,84 +73,191 @@
Output
All output files will be placed in the directory specified with -o
- GRAMPA creates three main output files and a filtered tree file (if necessary).
+ GRAMPA creates four output files, a log file, and a filtered tree file (if necessary).
GRAMPA also creates a directory within the output directory called groups_dir. This just stores the gene tree groupings for each MUL-tree
(in pickled format) so GRAMPA doesn't eat up a lot of RAM during
reconciliations. This can be ignored/deleted
- grampa_out.txt
- This is the main output file and contains some log info for the current run and it gives the total reconciliation score for each MUL-tree
- considered. At the bottom of the file it will display the MUL-tree with the minimum reconciliation score.
-
-# Tree # H1 node H2 node Tree string Total score
-ST (((a,(x,(y,z)<1>)<2>)<3>,b)<4>,(c,d)<5>)<6> 115
-MT-1 <2> a ((((a,(x*,(y*,z*)<1>)<2>)<3>,(x+,(y+,z+)<4>)<5>)<6>,b)<7>,(c,d)<8>)<9> 119
-MT-2 <2> c (((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,((c,(x*,(y*,z*)<5>)<6>)<7>,d)<8>)<9> 96
-MT-3 <2> b (((a,(x+,(y+,z+)<1>)<2>)<3>,(b,(x*,(y*,z*)<4>)<5>)<6>)<7>,(c,d)<8>)<9> 130
-MT-4 <2> d (((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(c,(d,(x*,(y*,z*)<5>)<6>)<7>)<8>)<9> 76
-MT-5 <2> <3> ((((a,(x+,(y+,z+)<1>)<2>)<3>,(x*,(y*,z*)<4>)<5>)<6>,b)<7>,(c,d)<8>)<9> 119
-MT-6 <2> <2> (((a,((x+,(y+,z+)<1>)<2>,(x*,(y*,z*)<3>)<4>)<5>)<6>,b)<7>,(c,d)<8>)<9> 145
-MT-7 <2> <6> ((((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(c,d)<5>)<6>,(x*,(y*,z*)<7>)<8>)<9> 132
-MT-8 <2> <4> ((((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(x*,(y*,z*)<5>)<6>)<7>,(c,d)<8>)<9> 118
-MT-9 <2> <5> (((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,((c,d)<5>,(x*,(y*,z*)<6>)<7>)<8>)<9> 95
-# ---------
-The MUL-tree with the minimum parsimony score is MT-4: (((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(c,(d,(x*,(y*,z*)<5>)<6>)<7>)<8>)<9>
-Score = 76
+ grampa-scores.txt
+ This is the main output file and contains the total reconciliation score for each MUL-tree considered, sorted in ascending order.
+
+
-
- - The first line has the headers for the columns of the output table. Note that H1 node and H2 node are always nodes in the singly
- labeled tree.
- - The total reconciliation score in the last column is the sum of all reconciliation scores for all gene trees for that MUL-tree.
-
-
+ The first line of this file contains the headers, defined as follows for each subsequent row:
+
+
+
+
+
+
+ mul.tree
+ h1.node
+ h2.node
+ score
+ mul.tree
+
+
+
+
+ The ID of the MUL-tree
+ The H1 node in the species tree for the current MUL-tree
+ The H2 node in the species tree for the current MUL-tree
+ The total parsimony score for the current MUL-tree
+ The Newick formatted tree string for the MUL-tree, with hybrid clades indicated with *
+
+
+
+
+
+
+ Please note that the input singly-labeled species tree always has the ID of 0
+
- grampa_det.txt
+ grampa-detailed.txt
The secondary output file contains detailed output describing the reconciliation scores from each gene tree to the lowest scoring MUL-tree.
-# MT-4:(((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(c,(d,(x*,(y*,z*)<5>)<6>)<7>)<8>)<9> H1 Node:<2> H2 Node:d
-# GT/MT combo # dups # losses Total score
-GT-1 to MT-4 1 1 2
-GT-2 to MT-4 1 2 3
-GT-3 to MT-4 1 3 4
-GT-4 to MT-4 1 2 3
-.
-.
-.
-GT-25 to MT-4 0 1 1
-# Gene trees with multiple maps: 1
-# Total parsimony score for MT-4: 76
+
- grampa_checknums.txt
+
+ The first line of this file contains the headers, defined as follows for each subsequent row:
+
+
+
+
+
+
+ mul.tree
+ gene.tree
+ dups
+ losses
+ total score
+
+
+
+
+ The ID of the MUL-tree
+ The ID of the gene tree being reconciled to the MUL-tree
+ The number of duplications on this gene tree given this MUL-tree
+ The number of losses on this gene tree given this MUL-tree
+ The sum of dups and losses for this gene tree and MUL-tree
+
+
+
+
+
+
+ Note that the lowest score for some GT/MT combos can have multiple maps. In these cases, we report all possible scores.
+
+
+ grampa-dup-counts.txt
+
+ For the 6 lowest scoring MUL-trees, GRAMPA counts the number of duplications along each branch in the MUL-tree summed
+ over all gene trees.
+
+
+
+ The first line of this file contains the headers, defined as follows for each subsequent row:
+
+
+
+
+
+
+ mul.tree
+ node
+ dups
+
+
+
+
+ The ID of the MUL-tree
+ The node ID for the current MUL-tree
+ The total number of duplications over all gene tres along the branch above the node in the MUL-tree
+
+
+
+
+
+ grampa-checknums.txt
GRAMPA must calculate how many combinations of maps there are for each gene-tree/MUL-tree pair and filter out those that are over
the group cap in any combo before any reconciliations can be done. This filtering ensures that all MUL-trees are reconciled to
the same set of gene-trees. The number of groups for each gene-tree/MUL-tree is recorded in this file.
-# GT/MT combo # Groups # Fixed # Combinations
-# MT-1:((((a,(x*,(y*,z*)<1>)<2>)<3>,(x+,(y+,z+)<4>)<5>)<6>,b)<7>,(c,d)<8>)<9> H1 Node:<2> H2 Node:a
-GT-1 to MT-1 2 0 4
-GT-2 to MT-1 1 1 2
-GT-3 to MT-1 1 1 2
-GT-4 to MT-1 1 1 2
-.
-.
-.
-GT-25 to MT-9 0 2 1
+
-
- - The first line in the file contains the table headers. For each MUL-tree there is also a line giving som info about it.
- - If a gene tree is over the cap specified with
-c X then the message Number of
- groups over group cap (-c set to X) -- Filtering. will also be displayed on the line.
-
-
+ The first line of this file contains the headers, defined as follows for each subsequent row:
+
+
+
+
+
+
+ mul.tree
+ gene.tree
+ groups
+ fixed
+ combinations
+ over.cap.filtered
+
+
+
+
+ The ID of the MUL-tree
+ The ID of the gene tree to be reconciled to the MUL-tree
+ The number of distinct hybrid clades in the gene tree
+ The number of hybrid clades in the gene tree that also group with a sister species from the singly-labeled tree
+ The total number of mappings to try for the gene tree with this MUL-tree
+ Either Y or N to indicate whether the number of groups exceeds the number set with -c
+
+
+
+
+
+ grampa-trees-filtered.txt
+
+ A text file with the gene trees used for this GRAMPA run, after filtering by the group cap. One tree per line.
+
+
+ grampa.log
+
+ A log file containing run time information and a summary of the lowest scoring MUL-tree.
+
@@ -189,10 +296,6 @@
A space separated list of nodes to search as possible parental lineages for all nodes specified with -h1.
If nothing is entered all possible nodes for the current h1 will be considered.
-s, -h1, and -h2.-s, -h1, and -h2 and write them to the log file.-c : The group cap(((a,(x,(y,z)<1>)<2>)<3>,b)<4>,(c,d)<5>)<6>--numtrees : Building MUL-trees+ This option quickly calculates how many MUL-trees are to be built with a given H1 and H2 set. If neither H1 or H2 are set + it will display the total number of MUL-trees possible for the input species tree. This information is printed to the screen. +
+--buildmultrees : Building MUL-treesThis option can be used with -s, -h1, and -h2 to build
@@ -389,6 +510,10 @@
Will yield the following output in the main output file (multree_ex/grampa_out.txt):
((((a,(x+,(y+,z+)<1>)<2>)<3>,b)<4>,(x*,(y*,z*)<5>)<6>)<7>,(c,d)<8>)<9>+ The MUL-trees are written to the log file. +
--checknums : Group counting-c.
+ --st-only : Group counting+ By default, GRAMPA reconciles the gene trees to all specified MUL-trees as well as the singly-labeled input species tree. Set this option to ONLY + do reconciliations to the singly-labeled input species tree. +
+--no-st : Group counting+ By default, GRAMPA reconciles the gene trees to all specified MUL-trees as well as the singly-labeled input species tree. Set this option to SKIP + reconciliations to the singly-labeled input species tree. +
+--maps : Output node mappingsSet this option to output the LCA node mappings along with the reconciliation scores to the detailed output file. This adds a column - to the _det.txt output file with that gene tree with the nodes re-labeled to include the maps, dups, and losses along that branch.
- -# GT/MT combo # dups # losses Total score Maps
-GT-1 to MT-4 1 1 2 (((1_a[a+-0],((1_x[x+-0],(1_y[y+-0],1_z[z+-0])<1>[<1>+-0])<2>[<2>+-0],(2_x[x+-0],(2_y[y+-0],2_z[z+-0])<3>[<1>+-0])<4>[<2>+-0])<5>[<2>+-1])<6>[<3>+-0],1_b[b+-0])<7>[<4>+-0],(1_c[c+-0],1_d[d+-0])<8>[<8>+-0])<9>[<9>+-0]
-GT-2 to MT-4 1 2 3 ((((1_a[a+-0],(1_x[x+-0],(1_y[y+-0],1_z[z+-0])<1>[<1>+-0])<2>[<2>+-0])<3>[<3>+-0],(2_x[x+-0],(2_y[y+-0],2_z[z+-0])<4>[<1>+-0])<5>[<2>+-0])<6>[<3>+-1],1_b[b+-0])<7>[<4>+-0],(1_c[c+-0],1_d[d+-0])<8>[<8>+-0])<9>[<9>+-0]
-GT-3 to MT-4 1 3 4 ((((1_a[a+-0],(1_x[x+-0],(1_y[y+-0],1_z[z+-0])<1>[<1>+-0])<2>[<2>+-0])<3>[<3>+-0],1_b[b+-0])<4>[<4>+-0],(2_x[x+-0],(2_y[y+-0],2_z[z+-0])<5>[<1>+-0])<6>[<2>+-0])<7>[<4>+-1],(1_c[c+-0],1_d[d+-0])<8>[<8>+-0])<9>[<9>+-0]
-GT-4 to MT-4 1 2 3 ((((1_a[a+-0],(2_x[x+-0],(2_y[y+-0],2_z[z+-0])<1>[<1>+-0])<2>[<2>+-0])<3>[<3>+-0],(1_x[x+-0],(1_y[y+-0],1_z[z+-0])<4>[<1>+-0])<5>[<2>+-0])<6>[<3>+-1],1_b[b+-0])<7>[<4>+-0],(1_c[c+-0],1_d[d+-0])<8>[<8>+-0])<9>[<9>+-0]
-
-.
-.
-.
-GT-25 to MT-4 0 1 1 (((1_a[a+-0],1_x[x+-0])<1>[<3>+-0],1_b[b+-0])<2>[<4>+-0],(1_c[c+-0],(1_d[d+-0],(2_x[x*-0],(1_y[y*-0],1_z[z*-0])<3>[<5>+-0])<4>[<6>+-0])<5>[<7>+-0])<6>[<8>+-0])<7>[<9>+-0]
-# Gene trees with multiple maps: 1
-# Total parsimony score for MT-4: 76
+
+ This option adds a column to the grampa-detailed.txt with the actual LCA node mappings for each gene tree and MUL-tree combo. The column
+ contains a Newick formatted version of the gene tree with nodes labeled as follows:
+
+
+ Node[Map-Dups]
+ Where Map indicates the node in the MUL-tree that this gene tree node maps to and Dups the number of duplications this mapping incurs. These trees
+ can be rendered with a tree viewer such as SeaView
+ or FigTree.
+
+