v0.1.5

Author: sungsik-kong

Manifest.toml

@@ -1,54 +1,19 @@
 PhyNEST: Phylogenetic Network Estimation using SiTe patterns
-Analysis start: 2023-03-24 at 08:10:42
-Input sequence file: example/scn2andgt20000.39.txt
-Number of sequences: 7 
-Sequence length: 2000000
-Starting Topology: (7,6,5,4,3,2,1);
-Outgroup specified for rooting: 7
-Number of maximum reticulation(s): 2
+Analysis start: 2023-05-16 at 11:55:29
+Input sequence file: example/sample_n5h1.txt
+Number of sequences: 5 
+Sequence length: 1000000
+Starting Topology: (5,(4,(3,(2,1))));
+Outgroup specified for rooting: 5
+Number of maximum reticulation(s): 1
 The maximum number of iterations for each optimization: 1000
 Search algorithm selected: Hill climbing
-The maximum number of steps during search: 1000000
+The maximum number of steps during search: 100000
 
-(1/15) Searching for the best network using the hill climbing algorithm...The search terminated at step 180 and at 100th consecutive failures.
-Summary of each move:
-Insertion of reticulation edge: 2 proposed, 2 accepted.
-Tail move of reticulation edge: 56 proposed, 2 accepted. 
-Head move of reticulation edge: 52 proposed, 0 accepted.
-Change the direction of reticulation edge: 27 proposed, 1 accepted.
-Deletion of reticulation edge: 0 proposed, 0 accepted.
-Nearest-neighbor interchange (NNI): 43 proposed, 1 accepted.
-On the current topology, 115 moves were made, including 15 unsuccessful moves.
-Terminated because it reached the maximum number of failures (current maximum_number_of_failures=100).
-(1/15) Estimated topology in this run: (7:5.858901865538142,(((((1:0.4895402649806814,(2:1.263190463023415)#H12:0.0::0.4954631266401886):0.7736501980427335,(3:0.4872669126554865,#H12:0.0::0.5045368733598115):0.7759235503679285):1.2442147399714147,4:2.5074052029948297):0.0,(5:0.0)#H9:0.0::0.4084401391767469):0.0,(6:0.325378144365268,#H9:0.0::0.5915598608232531):2.182027058629562):3.3514966625433122);
-(1/15) Composite likelihood of the estimated topology in this run: 6.405284917395862e7
+(1/2) Searching for the best network using the hill climbing algorithm...(1/2) Estimated topology in this run: (5:9.873012640463793,(4:4.978556362717051,((1:1.4303333981774915,#H6:1.4303333981774915::0.1):1.5674936103141652,((2:1.57039670220237)#H6:1.57039670220237::0.4753677704837127,3:1.57039670220237):1.4274303062892868):1.9807293542253945):4.894456277746742);
+(1/2) Composite likelihood of the estimated topology in this run: 4.7413446340573225e6
 
-(2/15) Searching for the best network using the hill climbing algorithm...(2/15) Terminated due to error
-
-(3/15) Searching for the best network using the hill climbing algorithm...(3/15) Terminated due to error
-
-(4/15) Searching for the best network using the hill climbing algorithm...(4/15) Terminated due to error
-
-(5/15) Searching for the best network using the hill climbing algorithm...(5/15) Terminated due to error
-
-(6/15) Searching for the best network using the hill climbing algorithm...(6/15) Terminated due to error
-
-(7/15) Searching for the best network using the hill climbing algorithm...(7/15) Terminated due to error
-
-(8/15) Searching for the best network using the hill climbing algorithm...(8/15) Terminated due to error
-
-(9/15) Searching for the best network using the hill climbing algorithm...(9/15) Terminated due to error
-
-(10/15) Searching for the best network using the hill climbing algorithm...(10/15) Terminated due to error
-
-(11/15) Searching for the best network using the hill climbing algorithm...(11/15) Terminated due to error
-
-(12/15) Searching for the best network using the hill climbing algorithm...(12/15) Terminated due to error
-
-(13/15) Searching for the best network using the hill climbing algorithm...(13/15) Terminated due to error
-
-(14/15) Searching for the best network using the hill climbing algorithm...(14/15) Terminated due to error
-
-(15/15) Searching for the best network using the hill climbing algorithm...(15/15) Terminated due to error
+(2/2) Searching for the best network using the hill climbing algorithm...(2/2) Estimated topology in this run: (5:10.2697095060683,(4:5.196775556882685,((3:2.357955465993553,(2:0.38031557369091684,(1:1.0000000000000006e-10)#H6:0.38031557369091684::0.3802733495916154):1.9776398923026361):1.2727612494513463,#H6:3.6307167154448994::0.6197266504083846):1.566058841437786):5.072933949185615);
+(2/2) Composite likelihood of the estimated topology in this run: 4.7413522473478215e6
 -----end of analysis
-Best topology: (7:5.858901865538142,(((((1:0.4895402649806814,(2:1.263190463023415)#H12:0.0::0.4954631266401886):0.7736501980427335,(3:0.4872669126554865,#H12:0.0::0.5045368733598115):0.7759235503679285):1.2442147399714147,4:2.5074052029948297):0.0,(5:0.0)#H9:0.0::0.4084401391767469):0.0,(6:0.325378144365268,#H9:0.0::0.5915598608232531):2.182027058629562):3.3514966625433122);
+Best topology: (5:9.873012640463793,(4:4.978556362717051,((1:1.4303333981774915,#H6:1.4303333981774915::0.1):1.5674936103141652,((2:1.57039670220237)#H6:1.57039670220237::0.4753677704837127,3:1.57039670220237):1.4274303062892868):1.9807293542253945):4.894456277746742);

PhyNEST_hc.log

@@ -13,4 +13,16 @@ The maximum number of steps during search: 100000
 (1/5) Searching for the best network using the simulated annealing algorithm...(1/5) Estimated topology in this run: (5:9.873014064438044,(4:4.978557142548183,((1:1.4303363486904264,#H6:1.4303363486904264::0.4753685835631588):1.5674911794711028,((2:1.5703948644162187)#H6:1.5703948644162187::0.5246314164368412,3:1.5703948644162187):1.4274326637453105):1.9807296143866542):4.89445692188986);
 (1/5) Composite likelihood of the estimated topology in this run: 4.741344634057322e6
 
-(2/5) Searching for the best network using the simulated annealing algorithm...
+(2/5) Searching for the best network using the simulated annealing algorithm...(2/5) Estimated topology in this run: (5:10.269709315698341,(4:5.196775448706899,(#H6:3.630716800952261::0.13894165235999334,(3:2.3579554127434714,(2:0.38031591472558735,(1:2.3579554127434714)#H6:0.38031591472558735::0.8610583476400067):1.9776394980178842):1.2727613882087896):1.5660586477546379):5.072933866991442);
+(2/5) Composite likelihood of the estimated topology in this run: 4.741352247347821e6
+
+(3/5) Searching for the best network using the simulated annealing algorithm...(3/5) Estimated topology in this run: (5:12.552567784501075,((4:6.449451813353731,(1:3.0371694627835937,(#H6:1.7529839521480117::0.12242718862590762,2:1.7529839521480117):1.284185510635582):3.412282350570137):0.0,(3:1.7529839521480117)#H6:6.449451813353731::0.8775728113740924):6.103115971147345);
+(3/5) Composite likelihood of the estimated topology in this run: 4.741455857605402e6
+
+(4/5) Searching for the best network using the simulated annealing algorithm...(4/5) Estimated topology in this run: (5:10.26970982380712,(4:5.196775729008606,(#H6:3.6307164574101316::0.02893974713192926,(3:2.3579555630912736,(2:0.3803146608614569,(1:2.3579555630912736)#H6:0.3803146608614569::0.9710602528680707):1.9776409022298167):1.272760894318858):1.5660592715984745):5.072934094798513);
+(4/5) Composite likelihood of the estimated topology in this run: 4.741352247347821e6
+
+(5/5) Searching for the best network using the simulated annealing algorithm...(5/5) Estimated topology in this run: (5:10.269711337269957,(4:5.196776531732105,(#H6:3.6307164821982667::0.2833610073201358,(3:2.3579560487611526,(2:0.3803134070427827,(1:2.3579560487611526)#H6:0.3803134070427827::0.7166389926798642):1.97764264171837):1.272760433437114):1.5660600495338386):5.072934805537852);
+(5/5) Composite likelihood of the estimated topology in this run: 4.7413522473478215e6
+-----end of analysis
+Best topology: (5:9.873014064438044,(4:4.978557142548183,((1:1.4303363486904264,#H6:1.4303363486904264::0.4753685835631588):1.5674911794711028,((2:1.5703948644162187)#H6:1.5703948644162187::0.5246314164368412,3:1.5703948644162187):1.4274326637453105):1.9807296143866542):4.89445692188986);

PhyNEST_sa.log

@@ -1,13 +1,14 @@
 name = "PhyNEST"
 uuid = "115de871-c282-4823-a74f-b03678acf966"
 authors = ["Sungsik Kong"]
-version = "0.1.4"
+version = "0.1.5"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterTools = "35a29f4d-8980-5a13-9543-d66fff28ecb8"

Project.toml

@@ -0,0 +1,35 @@
+PhyNEST: Phylogenetic Network Estimation using SiTe patterns
+Analysis start: 2023-05-15 at 14:36:54
+Input sequence file: sample_n5h1.txt
+Number of sequences: 5 
+Sequence length: 1000000
+Starting Topology: (5,(4,(3,(2,1))));
+Outgroup specified for rooting: 5
+Number of maximum reticulation(s): 1
+The maximum number of iterations for each optimization: 1000
+Search algorithm selected: Hill climbing
+The maximum number of steps during search: 100000
+
+(1/5) Searching for the best network using the hill climbing algorithm...The search terminated at step 94 and at 81th consecutive failures.
+Summary of each move:
+Insertion of reticulation edge: 2 proposed, 1 accepted.
+Tail move of reticulation edge: 27 proposed, 0 accepted. 
+Head move of reticulation edge: 29 proposed, 0 accepted.
+Change the direction of reticulation edge: 5 proposed, 1 accepted.
+Deletion of reticulation edge: 0 proposed, 0 accepted.
+Nearest-neighbor interchange (NNI): 30 proposed, 1 accepted.
+On the current topology, 96 moves were made, including 15 unsuccessful moves.
+Terminated although it neither reached the maximum number of steps or failures,
+possibly because there was no more move to make.
+(1/5) Estimated topology in this run: (5:9.873014355923681,(4:4.978557302744444,((3:1.5703960202935816,(2:1.4303350626712767)#H6:1.5703960202935816::0.5246318237325145):1.4274316184507447,(1:1.4303350626712767,#H6:1.4303350626712767::0.4753681762674855):1.5674925760730496):1.9807296640001177):4.894457053179237);
+(1/5) Composite likelihood of the estimated topology in this run: 4.7413446340573225e6
+
+(2/5) Searching for the best network using the hill climbing algorithm...(2/5) Terminated due to error
+
+(3/5) Searching for the best network using the hill climbing algorithm...(3/5) Terminated due to error
+
+(4/5) Searching for the best network using the hill climbing algorithm...(4/5) Terminated due to error
+
+(5/5) Searching for the best network using the hill climbing algorithm...(5/5) Terminated due to error
+-----end of analysis
+Best topology: (5:9.873014355923681,(4:4.978557302744444,((3:1.5703960202935816,(2:1.4303350626712767)#H6:1.5703960202935816::0.5246318237325145):1.4274316184507447,(1:1.4303350626712767,#H6:1.4303350626712767::0.4753681762674855):1.5674925760730496):1.9807296640001177):4.894457053179237);