Add Vercel configuration for rewrites and build settings

2025-12-17 17:47:45 +08:00
parent 072524e303
commit 0d31d42de4
32 changed files with 7435 additions and 289 deletions
@@ -0,0 +1,150 @@
+---
+layout: section
+color: navy
+---
+
+<div class="w-7/10 mx-auto text-center">
+
+## 技术路线与分析进展
+
+<hr/>
+
+当前分析进展情况
+
+</div>
+
+---
+layout: side-title
+color: navy
+align: rm-lm
+titlewidth: is-3
+title: 技术路线图（上）
+
+---
+
+::title::
+
+# 技术路线图（上）
+
+::content::
+
+```mermaid
+flowchart TD
+
+classDef default fill:#ECF5FF,stroke:#409eff,stroke-width:2px,color:#409eff;
+classDef done fill:#F0F9EB,stroke:#67c23a,stroke-width:2px,color:#67c23a;
+classDef warn fill:#FDF6EC,stroke:#e6a23c,stroke-width:2px,color:#e6a23c
+
+subgraph subgraph1[Step1. 数据预处理与组装]
+    direction LR
+    RawData[原始数据，来自sra]:::warn --> CleanData[数据清洗与质控，Fastp]:::done
+    CleanData -- 沙棘样品，有参 --> AlignData[比对到参考基因组，Hisat2]:::done
+    AlignData --> Assembly[组装成转录本，Trinity]:::done
+    CleanData -- 胡颓子，无参 --> Assembly[组装成转录本，使用N50和busco评估组装结果，Trinity]:::done
+end
+
+subgraph subgraph2[Step2. 同源基因集聚类]
+    direction LR
+    ass[转录本]:::warn --> CDS[预测CDS，抽取最长转录本的最长ORF作为输入CDS，TransDecoder]:::done
+    CDS --> reducedCDS[单样本CDS序列去冗余，CD-HIT]:::done
+    reducedCDS --> ortho[基因家族聚类得到低拷贝同源基因集，OrthoFinder]:::done
+    ortho --> homolog[将枣的同源基因整合到低拷贝同源基因集中, hmmer]:::done
+end
+
+subgraph subgraph3[Step3. 基因集筛选与基因树]
+    direction LR
+    homo[低拷贝同源基因集]:::warn --> alignment[基于蛋白序列比对，mafft/pal2nal<br>修剪比对序列，trimAl]:::done
+    alignment --> treeshrink[fasttree快速构树，基于长枝吸引（treeshrink）和比对序列长度过滤基因集]:::done
+    treeshrink --> modeltest[序列进化模型检验，modeltest-ng]:::done
+    modeltest --> raxml[构建ML单基因树]:::done
+    modeltest --> mrbayes[构建BP单基因树]:::done
+    raxml --> trees[根据mrbayes的结果收敛性筛选基因树与对应序列]:::done
+    mrbayes --> trees
+end
+
+subgraph subgraph4[Step4. 物种系统发育关系]
+    direction LR
+    tree[过滤后单基因树与对应序列]:::warn -- 单基因ML树 --> coalescence[溯祖关系树, Aster]
+    tree -- 单基因ML树 --> phyparts[基因树不一致性展示]
+    tree -- 单基因序列 --> concatenation[串联关系树，iqtree3]
+    tree -- 单基因的mrbayes分析结果 --> CFs[基因树一致性因子，BUCKy]:::done
+    CFs --> network[系统发育网络，SNAQ]:::done
+    coalescence --> network
+end
+
+subgraph note[节点说明]
+    direction TB
+    done[已完成分析]:::done
+    warn[重要中间数据]:::warn
+    default[未完成分析]
+end
+
+subgraph1 --> subgraph2
+subgraph2 --> subgraph3
+subgraph3 --> subgraph4
+subgraph4 ~~~ note
+```
+
+---
+layout: side-title
+color: navy
+align: rm-lm
+titlewidth: is-3
+title: 技术路线图（下）
+
+---
+
+::title::
+# 技术路线图（下）
+
+::content::
+
+```mermaid
+flowchart TD
+
+classDef default fill:#ECF5FF,stroke:#409eff,stroke-width:2px,color:#409eff;
+classDef done fill:#F0F9EB,stroke:#67c23a,stroke-width:2px,color:#67c23a;
+classDef warn fill:#FDF6EC,stroke:#e6a23c,stroke-width:2px,color:#e6a23c
+
+subgraph subgraph5[Step5. 叶绿体系统发育关系]
+    direction LR
+    cleanData[Clean Reads]:::done --> alignCp[比对到参考叶绿体基因组，hisat2]:::done
+    alignCp --> callExon[提取比对上的外显子序列，samtools]
+    callExon --> cpTree[串联高质量的exon片段，构建叶绿体基因组系统发育树，iqtree3]
+    cpTree --> divergence[估算叶绿体基因组分歧时间，beast]
+end
+
+subgraph subgraph6[Step6. 沙棘模型分析]
+    direction LR
+    genes[筛选得到的低拷贝同源基因集]:::warn --> filterGenes[基于ml树筛选基因集用于后续模型]
+    filterGenes --> mcmcTree[使用mcmctree估算分化时间]
+    mcmcTree --> fitModel[使用模型拟合种间分化时间分布]
+    fitModel --> integrate[整合不同模型结果得到最终分化时间估计]
+end
+
+subgraph subgraph7[Step7. bpp模拟模型分析]
+    direction LR
+    bpp[使用bpp进行溯祖模拟得到基因集]:::warn --> mcmcTreeBPP[使用mcmctree估算分化时间]
+    mcmcTreeBPP --> fitModelBPP[使用模型拟合种间分化时间分布]
+    fitModelBPP --> integrateBPP[整合不同模型结果得到最终分化时间估计]
+end
+
+subgraph subgraph8[Step8. 蛇数据分析]
+    direction LR
+    snakeData[蛇数据]:::warn --> mcmcTreeSnake[使用mcmctree估算分化时间]
+    mcmcTreeSnake --> fitModelSnake[使用模型拟合种间分化时间分布]
+    fitModelSnake --> integrateSnake[整合不同模型结果得到最终分化时间估计]
+end
+
+subgraph note[节点说明]
+    direction TB
+    done[已完成分析]:::done
+    warn[重要中间数据]:::warn
+    default[未完成分析]
+end
+
+subgraph5 --> subgraph6
+subgraph6 --> subgraph7
+subgraph7 --> subgraph8
+subgraph8 ~~~ note
+```