From b9db03cca99524b7c0db191f4689f74262d45850 Mon Sep 17 00:00:00 2001 From: HuaiyanRen <928003585@qq.com> Date: Tue, 11 Aug 2026 15:03:48 +1000 Subject: [PATCH 1/6] Update PartitionFinder-mAIC --- doc/Advanced-Tutorial.md | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/doc/Advanced-Tutorial.md b/doc/Advanced-Tutorial.md index d64b32c..c9bf88f 100644 --- a/doc/Advanced-Tutorial.md +++ b/doc/Advanced-Tutorial.md @@ -143,8 +143,7 @@ Choosing the right partitioning scheme --------------------------------------
-ModelFinder implements a greedy strategy ([Lanfear et al., 2012]) that starts with the full partition model and subsequentially -merges two genes until the model fit does not increase any further: +ModelFinder integrates the PartitionFinder algorithm ([Lanfear et al., 2012]) that starts with the full partition model and subsequently merges two partition subsets until the model fit does not increase any further: iqtree -s example.phy -p example.nex -m MFP+MERGE # for version 1.x change -p to -spp @@ -166,16 +165,16 @@ To resemble PartitionFinder and save time: iqtree -s example.phy -p example.nex -m TESTMERGEONLY # for version 1.x change -p to -spp +This implementation includes a greedy algorithm ([Lanfear et al., 2012]) that subsequentially merges a single pair of subsets per iteration, and a *relaxed hierarchical clustering algorithm* (default; [Lanfear et al., 2014]) that merges multiple pairs of subsets per iteration to reduce the computational burden. Starting with version 3.1.3, PartitionFinder by default applies marginal Akaike Information Criterion (mAIC; [Susko et al., 2026]) as the criterion for partition merging. If you use PartitionFinder-mAIC in a publication, please cite: -To reduce the computational burden IQ-TREE implements the *relaxed hierarchical clustering algorithm* ([Lanfear et al., 2014]), which is invoked via `-rcluster` option: - - iqtree -s example.phy -p example.nex -m MF+MERGE -rcluster 10 - # for version 1.x change -p to -spp - - -to only examine the top 10% partition merging schemes (similar to the `--rcluster-percent 10` option in PartitionFinder). - +> TBD +Here are the options to specify the detail of PartitionFinder algorithm: +| Option | Description | +| ------------ | ---------------------------------------------------------------------- | +| `--merge` | Specify either `rcluster` or `greedy` algorithm. *DEFAULT: `rcluster`* | +| `--rcluster` | Specify the percentage of top partition merging schemes. *DEFAULT: 10* | +| `-merit` | Specify either `mAIC`, `AIC`,`AICc` or `BIC` for partition merging criterion. *DEFAULT: `mAIC`* | Ultrafast bootstrapping with partition model -------------------------------------------- @@ -587,6 +586,7 @@ See [Command Reference](Command-Reference) for a complete list of all options av [Kishino and Hasegawa, 1989]: https://doi.org/10.1007/BF02100115 [Lanfear et al., 2012]: https://doi.org/10.1093/molbev/mss020 [Lanfear et al., 2014]: https://doi.org/10.1186/1471-2148-14-82 +[Susko et al., 2026]: https://doi.org/10.1093/sysbio/syag013 [Lopez et al., 2002]: http://mbe.oxfordjournals.org/content/19/1/1.full [Nei et al., 2001]: https://doi.org/10.1073/pnas.051611498 [Seo et al., 2005]: https://doi.org/10.1073/pnas.0408313102 From 711bf16c26ffc01231919143ec978364697ad884 Mon Sep 17 00:00:00 2001 From: HuaiyanRen <928003585@qq.com> Date: Tue, 11 Aug 2026 15:12:08 +1000 Subject: [PATCH 2/6] Update Advanced-Tutorial.md --- doc/Advanced-Tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/Advanced-Tutorial.md b/doc/Advanced-Tutorial.md index c9bf88f..2159723 100644 --- a/doc/Advanced-Tutorial.md +++ b/doc/Advanced-Tutorial.md @@ -173,7 +173,7 @@ Here are the options to specify the detail of PartitionFinder algorithm: | Option | Description | | ------------ | ---------------------------------------------------------------------- | | `--merge` | Specify either `rcluster` or `greedy` algorithm. *DEFAULT: `rcluster`* | -| `--rcluster` | Specify the percentage of top partition merging schemes. *DEFAULT: 10* | +| `--rcluster` | Specify the percentage of most similar candidate partition pairs retained for merging at each iteration (relaxed clustering algorithm only). *DEFAULT: 10* | | `-merit` | Specify either `mAIC`, `AIC`,`AICc` or `BIC` for partition merging criterion. *DEFAULT: `mAIC`* | Ultrafast bootstrapping with partition model From 9ae29ad39b85b5dfb70e2ad9cea62cc574df6051 Mon Sep 17 00:00:00 2001 From: HuaiyanRen <928003585@qq.com> Date: Tue, 11 Aug 2026 15:13:51 +1000 Subject: [PATCH 3/6] Update Advanced-Tutorial.md --- doc/Advanced-Tutorial.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/Advanced-Tutorial.md b/doc/Advanced-Tutorial.md index 2159723..c70b2a8 100644 --- a/doc/Advanced-Tutorial.md +++ b/doc/Advanced-Tutorial.md @@ -172,9 +172,10 @@ This implementation includes a greedy algorithm ([Lanfear et al., 2012]) that su Here are the options to specify the detail of PartitionFinder algorithm: | Option | Description | | ------------ | ---------------------------------------------------------------------- | +| `-merit` | Specify either `mAIC`, `AIC`,`AICc` or `BIC` for partition merging criterion. *DEFAULT: `mAIC`* | | `--merge` | Specify either `rcluster` or `greedy` algorithm. *DEFAULT: `rcluster`* | | `--rcluster` | Specify the percentage of most similar candidate partition pairs retained for merging at each iteration (relaxed clustering algorithm only). *DEFAULT: 10* | -| `-merit` | Specify either `mAIC`, `AIC`,`AICc` or `BIC` for partition merging criterion. *DEFAULT: `mAIC`* | + Ultrafast bootstrapping with partition model -------------------------------------------- From 3cf036d90e2e42e921c99b63b015ba0c999017e5 Mon Sep 17 00:00:00 2001 From: HuaiyanRen <928003585@qq.com> Date: Wed, 19 Aug 2026 14:45:46 +1000 Subject: [PATCH 4/6] Update PartitionFinder details --- doc/Advanced-Tutorial.md | 29 ++++++++++++++++++++--------- 1 file changed, 20 insertions(+), 9 deletions(-) diff --git a/doc/Advanced-Tutorial.md b/doc/Advanced-Tutorial.md index c70b2a8..6cb95d7 100644 --- a/doc/Advanced-Tutorial.md +++ b/doc/Advanced-Tutorial.md @@ -165,17 +165,27 @@ To resemble PartitionFinder and save time: iqtree -s example.phy -p example.nex -m TESTMERGEONLY # for version 1.x change -p to -spp -This implementation includes a greedy algorithm ([Lanfear et al., 2012]) that subsequentially merges a single pair of subsets per iteration, and a *relaxed hierarchical clustering algorithm* (default; [Lanfear et al., 2014]) that merges multiple pairs of subsets per iteration to reduce the computational burden. Starting with version 3.1.3, PartitionFinder by default applies marginal Akaike Information Criterion (mAIC; [Susko et al., 2026]) as the criterion for partition merging. If you use PartitionFinder-mAIC in a publication, please cite: - +Starting with version 3.1.3, PartitionFinder by default applies the marginal Akaike Information Criterion (mAIC; [Susko et al., 2026]) as the criterion for partition merging. If you use PartitionFinder-mAIC in a publication, please cite: > TBD -Here are the options to specify the detail of PartitionFinder algorithm: -| Option | Description | -| ------------ | ---------------------------------------------------------------------- | -| `-merit` | Specify either `mAIC`, `AIC`,`AICc` or `BIC` for partition merging criterion. *DEFAULT: `mAIC`* | -| `--merge` | Specify either `rcluster` or `greedy` algorithm. *DEFAULT: `rcluster`* | -| `--rcluster` | Specify the percentage of most similar candidate partition pairs retained for merging at each iteration (relaxed clustering algorithm only). *DEFAULT: 10* | +PartitionFinder implementation includes four merging algorithms, which differ in how thoroughly they search the space of partitioning schemes and how many pairs they merge per iteration: + +| Algorithm | IQ-TREE Command | Description | Reference | +| ------------------------------------ | --------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | +| Greedy | `greedy` | At each iteration, evaluates all candidate subset pairs and merges the single pair that gives the best information-criterion score. | [Lanfear et al., 2012] | +| Relaxed hierarchical clustering | `rcluster` | At each iteration, evaluates only the top k% most similar candidate subset pairs and merges the best-scoring one. | [Lanfear et al., 2014] | +| Fast hierarchical relaxed clustering | `rclusterf` | At each iteration, evaluates only the top k% most similar candidate subset pairs and merges multiple compatible pairs at once. (IQ-TREE default). | [Lanfear et al., 2014] | +| k-means | `kmeans` | Estimates an evolutionary rate for each site, then iteratively clusters individual sites by rate using k-means, without relying on predefined data blocks. | [Frandsen et al., 2015] | + +The following options control the details of the merging procedure: +| Option | Description | +| ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | +| `-merit` | Specify either `mAIC`, `AIC`, `AICc` or `BIC` for the partition merging criterion. *DEFAULT: `mAIC`* | +| `--merge` | Specify either `rclusterf`, `rcluster`, `greedy` or `kmeans` algorithm. *DEFAULT: `rclusterf`* | +| `--rclusterf` | Specify the percentage of most similar candidate partition pairs retained for merging at each iteration (this automatically selects the fast relaxed clustering algorithm). *DEFAULT: 10* | +| `--rcluster` | Specify the percentage of most similar candidate partition pairs retained for merging at each iteration (this automatically selects the relaxed clustering algorithm). *DEFAULT: 10* | +| `--rcluster-max` | Specify the maximum number of most similar candidate partition pairs retained for merging at each iteration (only for the fast relaxed clustering and relaxed clustering algorithms). *DEFAULT: 10 × number of partitions in the full partition model* | Ultrafast bootstrapping with partition model -------------------------------------------- @@ -586,8 +596,9 @@ See [Command Reference](Command-Reference) for a complete list of all options av [Kishino et al., 1990]: https://doi.org/10.1007/BF02109483 [Kishino and Hasegawa, 1989]: https://doi.org/10.1007/BF02100115 [Lanfear et al., 2012]: https://doi.org/10.1093/molbev/mss020 -[Lanfear et al., 2014]: https://doi.org/10.1186/1471-2148-14-82 [Susko et al., 2026]: https://doi.org/10.1093/sysbio/syag013 +[Lanfear et al., 2014]: https://doi.org/10.1186/1471-2148-14-82 +[Frandsen et al., 2015]: https://doi.org/10.1186/s12862-015-0283-7 [Lopez et al., 2002]: http://mbe.oxfordjournals.org/content/19/1/1.full [Nei et al., 2001]: https://doi.org/10.1073/pnas.051611498 [Seo et al., 2005]: https://doi.org/10.1073/pnas.0408313102 From cba6bdad3e16634bf109e4b15e223a354429d540 Mon Sep 17 00:00:00 2001 From: HuaiyanRen <928003585@qq.com> Date: Wed, 19 Aug 2026 15:00:40 +1000 Subject: [PATCH 5/6] Update PartitionFinder --- doc/Advanced-Tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/Advanced-Tutorial.md b/doc/Advanced-Tutorial.md index 6cb95d7..973b5f0 100644 --- a/doc/Advanced-Tutorial.md +++ b/doc/Advanced-Tutorial.md @@ -181,7 +181,7 @@ The following options control the details of the merging procedure: | Option | Description | | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -| `-merit` | Specify either `mAIC`, `AIC`, `AICc` or `BIC` for the partition merging criterion. *DEFAULT: `mAIC`* | +| `-merit` | Specify either `mAIC`, `AIC`, `AICc` or `BIC` for the partition merging criterion. *Defaults to `mAIC` when `MERGE` is enabled; defaults to `BIC` for stardard model selection.* | | `--merge` | Specify either `rclusterf`, `rcluster`, `greedy` or `kmeans` algorithm. *DEFAULT: `rclusterf`* | | `--rclusterf` | Specify the percentage of most similar candidate partition pairs retained for merging at each iteration (this automatically selects the fast relaxed clustering algorithm). *DEFAULT: 10* | | `--rcluster` | Specify the percentage of most similar candidate partition pairs retained for merging at each iteration (this automatically selects the relaxed clustering algorithm). *DEFAULT: 10* | From a8404ac875791d1dc057ea9091b9e2852c7e4f06 Mon Sep 17 00:00:00 2001 From: HuaiyanRen <928003585@qq.com> Date: Wed, 26 Aug 2026 11:12:06 +1000 Subject: [PATCH 6/6] Set BIC default for PartitionFinder --- doc/Advanced-Tutorial.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/doc/Advanced-Tutorial.md b/doc/Advanced-Tutorial.md index 973b5f0..59d1e97 100644 --- a/doc/Advanced-Tutorial.md +++ b/doc/Advanced-Tutorial.md @@ -165,7 +165,11 @@ To resemble PartitionFinder and save time: iqtree -s example.phy -p example.nex -m TESTMERGEONLY # for version 1.x change -p to -spp -Starting with version 3.1.3, PartitionFinder by default applies the marginal Akaike Information Criterion (mAIC; [Susko et al., 2026]) as the criterion for partition merging. If you use PartitionFinder-mAIC in a publication, please cite: +Starting with version 3.1.4, PartitionFinder supports the marginal Akaike Information Criterion (mAIC; [Susko et al., 2026]) as an optional criterion for partition merging. To apply PartitionFinder-mAIC: + + iqtree -s example.phy -p example.nex -m MFP+MERGE -merit mAIC + +If you use PartitionFinder-mAIC in a publication, please cite: > TBD PartitionFinder implementation includes four merging algorithms, which differ in how thoroughly they search the space of partitioning schemes and how many pairs they merge per iteration: @@ -181,7 +185,7 @@ The following options control the details of the merging procedure: | Option | Description | | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -| `-merit` | Specify either `mAIC`, `AIC`, `AICc` or `BIC` for the partition merging criterion. *Defaults to `mAIC` when `MERGE` is enabled; defaults to `BIC` for stardard model selection.* | +| `-merit` | Specify either `AIC`, `AICc`, `BIC` or `mAIC` for the partition merging criterion. *DEFAULT: `BIC`* | | `--merge` | Specify either `rclusterf`, `rcluster`, `greedy` or `kmeans` algorithm. *DEFAULT: `rclusterf`* | | `--rclusterf` | Specify the percentage of most similar candidate partition pairs retained for merging at each iteration (this automatically selects the fast relaxed clustering algorithm). *DEFAULT: 10* | | `--rcluster` | Specify the percentage of most similar candidate partition pairs retained for merging at each iteration (this automatically selects the relaxed clustering algorithm). *DEFAULT: 10* |