update readme

zhangrengang · Sep 25, 2024 · ecc8048 · ecc8048
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diff --git a/README.md b/README.md
@@ -395,7 +395,8 @@ Tetracendron_sinense|Tesin01G0062600    Trochodendron_aralioides|evm.TU.group9.7
 ```
 
 #### Orthology format ####
-The outputs from [OrthoFinder2](https://github.com/davidemms/OrthoFinder) and OrthoMCL are supported:
+The outputs from [OrthoFinder2](https://github.com/davidemms/OrthoFinder), OrthoMCL, 
+[Broccoli](https://github.com/rderelle/Broccoli), [SonicParanoid2](https://gitlab.com/salvo981/sonicparanoid2) are supported:
 ```
 # OrthoFinder2 output directory like:
 OrthoFinder/OrthoFinder/Results_Jun25/
@@ -409,7 +410,7 @@ Tetracendron_sinense|Tesin01G0060800    Trochodendron_aralioides|evm.TU.group9.7
 ```
 
 #### Gene coordinate format ####
-The gff/bed format for JCVI, MCscanX and WGDI are also supported:
+The gff/bed format for JCVI, MCscanX and WGDI are supported:
 ```
 # gff for WGDI:
 Dc1     Daucus_carota|DCAR_000504       20809   26333   +       1       Daucus_carota|DCAR_000504

diff --git a/evolution_example b/evolution_example
diff --git a/soi/__version__.py b/soi/__version__.py
@@ -1 +1 @@
-version = '1.0.5'
+version = '1.1'
+76 −31		README.md
+2 −2		wgdi/Angelica_sinensis-Angelica_sinensis.conf.gz
+2 −2		wgdi/Angelica_sinensis-Apium_graveolens.conf.gz
+2 −2		wgdi/Angelica_sinensis-Aralia_elata.conf.gz
+2 −2		wgdi/Angelica_sinensis-Centella_asiatica.conf.gz
+2 −2		wgdi/Angelica_sinensis-Coriandrum_sativum.conf.gz
+2 −2		wgdi/Angelica_sinensis-Eleutherococcus_senticosus.conf.gz
+2 −2		wgdi/Angelica_sinensis-Ilex_polyneura.conf.gz
+2 −2		wgdi/Angelica_sinensis-Lonicera_japonica.conf.gz
+2 −2		wgdi/Angelica_sinensis-Panax_ginseng.conf.gz
+2 −2		wgdi/Angelica_sinensis-Panax_notoginseng.conf.gz
+2 −2		wgdi/Angelica_sinensis-Vitis_vinifera.conf.gz
+2 −2		wgdi/Apium_graveolens-Apium_graveolens.conf.gz
+2 −2		wgdi/Apium_graveolens-Aralia_elata.conf.gz
+2 −2		wgdi/Apium_graveolens-Centella_asiatica.conf.gz
+2 −2		wgdi/Apium_graveolens-Coriandrum_sativum.conf.gz
+2 −2		wgdi/Apium_graveolens-Eleutherococcus_senticosus.conf.gz
+2 −2		wgdi/Apium_graveolens-Ilex_polyneura.conf.gz
+2 −2		wgdi/Apium_graveolens-Lonicera_japonica.conf.gz
+2 −2		wgdi/Apium_graveolens-Panax_ginseng.conf.gz
+2 −2		wgdi/Apium_graveolens-Panax_notoginseng.conf.gz
+2 −2		wgdi/Apium_graveolens-Vitis_vinifera.conf.gz
+2 −2		wgdi/Aralia_elata-Aralia_elata.conf.gz
+2 −2		wgdi/Aralia_elata-Eleutherococcus_senticosus.conf.gz
+2 −2		wgdi/Aralia_elata-Ilex_polyneura.conf.gz
+2 −2		wgdi/Aralia_elata-Lonicera_japonica.conf.gz
+2 −2		wgdi/Aralia_elata-Panax_ginseng.conf.gz
+2 −2		wgdi/Aralia_elata-Panax_notoginseng.conf.gz
+2 −2		wgdi/Aralia_elata-Vitis_vinifera.conf.gz
+2 −2		wgdi/Centella_asiatica-Aralia_elata.conf.gz
+2 −2		wgdi/Centella_asiatica-Centella_asiatica.conf.gz
+2 −2		wgdi/Centella_asiatica-Eleutherococcus_senticosus.conf.gz
+2 −2		wgdi/Centella_asiatica-Ilex_polyneura.conf.gz
+2 −2		wgdi/Centella_asiatica-Lonicera_japonica.conf.gz
+2 −2		wgdi/Centella_asiatica-Panax_ginseng.conf.gz
+2 −2		wgdi/Centella_asiatica-Panax_notoginseng.conf.gz
+2 −2		wgdi/Centella_asiatica-Vitis_vinifera.conf.gz
+2 −2		wgdi/Coriandrum_sativum-Aralia_elata.conf.gz
+2 −2		wgdi/Coriandrum_sativum-Centella_asiatica.conf.gz
+2 −2		wgdi/Coriandrum_sativum-Coriandrum_sativum.conf.gz
+2 −2		wgdi/Coriandrum_sativum-Eleutherococcus_senticosus.conf.gz
+2 −2		wgdi/Coriandrum_sativum-Ilex_polyneura.conf.gz
+2 −2		wgdi/Coriandrum_sativum-Lonicera_japonica.conf.gz
+2 −2		wgdi/Coriandrum_sativum-Panax_ginseng.conf.gz
+2 −2		wgdi/Coriandrum_sativum-Panax_notoginseng.conf.gz
+2 −2		wgdi/Coriandrum_sativum-Vitis_vinifera.conf.gz
+2 −2		wgdi/Daucus_carota-Angelica_sinensis.conf.gz
+2 −2		wgdi/Daucus_carota-Apium_graveolens.conf.gz
+2 −2		wgdi/Daucus_carota-Aralia_elata.conf.gz
+2 −2		wgdi/Daucus_carota-Centella_asiatica.conf.gz
+2 −2		wgdi/Daucus_carota-Coriandrum_sativum.conf.gz
+2 −2		wgdi/Daucus_carota-Daucus_carota.conf.gz
+2 −2		wgdi/Daucus_carota-Eleutherococcus_senticosus.conf.gz
+2 −2		wgdi/Daucus_carota-Ilex_polyneura.conf.gz
+2 −2		wgdi/Daucus_carota-Lonicera_japonica.conf.gz
+2 −2		wgdi/Daucus_carota-Panax_ginseng.conf.gz
+2 −2		wgdi/Daucus_carota-Panax_notoginseng.conf.gz
+2 −2		wgdi/Daucus_carota-Vitis_vinifera.conf.gz
+2 −2		wgdi/Eleutherococcus_senticosus-Eleutherococcus_senticosus.conf.gz
+2 −2		wgdi/Eleutherococcus_senticosus-Ilex_polyneura.conf.gz
+2 −2		wgdi/Eleutherococcus_senticosus-Lonicera_japonica.conf.gz
+2 −2		wgdi/Eleutherococcus_senticosus-Panax_ginseng.conf.gz
+2 −2		wgdi/Eleutherococcus_senticosus-Panax_notoginseng.conf.gz
+2 −2		wgdi/Eleutherococcus_senticosus-Vitis_vinifera.conf.gz
+2 −2		wgdi/Ilex_polyneura-Ilex_polyneura.conf.gz
+2 −2		wgdi/Ilex_polyneura-Vitis_vinifera.conf.gz
+2 −2		wgdi/Lonicera_japonica-Ilex_polyneura.conf.gz
+2 −2		wgdi/Lonicera_japonica-Lonicera_japonica.conf.gz
+2 −2		wgdi/Lonicera_japonica-Vitis_vinifera.conf.gz
+2 −2		wgdi/Panax_ginseng-Ilex_polyneura.conf.gz
+2 −2		wgdi/Panax_ginseng-Lonicera_japonica.conf.gz
+2 −2		wgdi/Panax_ginseng-Panax_ginseng.conf.gz
+2 −2		wgdi/Panax_ginseng-Panax_notoginseng.conf.gz
+2 −2		wgdi/Panax_ginseng-Vitis_vinifera.conf.gz
+2 −2		wgdi/Panax_notoginseng-Ilex_polyneura.conf.gz
+2 −2		wgdi/Panax_notoginseng-Lonicera_japonica.conf.gz
+2 −2		wgdi/Panax_notoginseng-Panax_notoginseng.conf.gz
+2 −2		wgdi/Panax_notoginseng-Vitis_vinifera.conf.gz
+2 −2		wgdi/Vitis_vinifera-Vitis_vinifera.conf.gz