Further mesh research: create an individual mesh for each animation sequence, with a single blend shape animation per mesh. Added an AliasModel class to manage meshes and find the correct animations. With this we can smoothly animate looped animation cycles.

Assets/Scripts/Modules/AliasModel.cs

@@ -0,0 +1,53 @@
+using System.Collections.Generic;
+using System.Text.RegularExpressions;
+using UnityEngine;
+
+public class AliasModel
+{
+    public static readonly Regex AnimationRegex = new Regex(@"^[a-zA-Z]+");
+    
+    private readonly List<(int, Mesh)> animationMeshes = new List<(int, Mesh)>();   // TODO: make this a fixed array after initialization
+
+    public void AddAnimation(int startFrame, Mesh mesh)
+    {
+        animationMeshes.Add((startFrame, mesh));
+    }
+
+    public int GetAnimationFrameCount(float frameNum)
+    {
+        if (!FindAnimation((int)frameNum, out Mesh mesh, out int startFrame))
+            return 0;
+
+        return mesh.GetBlendShapeFrameCount(0);
+    }
+
+    public void Animate(float frameNum, out Mesh mesh, out float blendWeight)
+    {
+        blendWeight = 0;
+        
+        int frameIndex = (int)frameNum;
+        if (!FindAnimation(frameIndex, out mesh, out int startFrame))
+            return;
+
+        int numFrames = mesh.GetBlendShapeFrameCount(0);
+        blendWeight = ((frameNum - startFrame) / numFrames) % 1;
+    }
+
+    private bool FindAnimation(int frameIndex, out Mesh mesh, out int startFrame)
+    {
+        mesh = null;
+        startFrame = 0;
+        
+        for (int i = 0; i < animationMeshes.Count; ++i)
+        {
+            startFrame = animationMeshes[i].Item1;
+            if (frameIndex >= startFrame)
+            {
+                mesh = animationMeshes[i].Item2;
+                return true;
+            }
+        }
+
+        return false;   // Shouldn't happen
+    }
+}

Assets/Scripts/Modules/AliasModel.cs.meta

@@ -0,0 +1,3 @@
+fileFormatVersion: 2
+guid: 74fb95086b6c4400bc3696481e4679e6
+timeCreated: 1618650253

Assets/Scripts/Modules/AliasModelAnimator.cs

@@ -3,6 +3,8 @@ using UnityEngine;
 
 public class AliasModelAnimator : MonoBehaviour
 {
+    public AliasModel aliasModel;
+    
     //private int frameNumber = 0;
     private float frameNumber = 0;
 
@@ -15,19 +17,19 @@ public class AliasModelAnimator : MonoBehaviour
             yield break;
         }
 
-        var mesh = meshRenderer.sharedMesh;
-        int numFrames = mesh.GetBlendShapeFrameCount(0);
+        int numFrames = aliasModel.GetAnimationFrameCount(0);
 
         while (true)
         {
-            float blendWeight = (float)frameNumber / numFrames;
+            aliasModel.Animate(frameNumber, out Mesh mesh, out float blendWeight);
+            meshRenderer.sharedMesh = mesh;
             meshRenderer.SetBlendShapeWeight(0, blendWeight);
 
             //yield return new WaitForSeconds(0.1f); // Animate at 10 fps
             yield return null;
 
             //frameNumber = (frameNumber + 1) % numFrames;
-            frameNumber = (frameNumber + Time.deltaTime * 10) % numFrames;
+            frameNumber = (frameNumber + Time.deltaTime * 5) % numFrames;
         }
     }
 }

Assets/Scripts/Modules/RenderModule.cs

@@ -18,21 +18,36 @@ public partial class RenderModule
     {
         Debug.Log($"Alias model '{name}' with {header.numVerts} vertices, {header.numTriangles} triangles, {header.numFrames} frame(s)");
 
-        ConvertVertices(header, poseVertices[0], out var vertices, out var normals);
         ConvertTriangles(triangles, out var indices);
         ConvertUVs(stVertices, header.skinWidth, header.skinHeight, out var uvs);
 
-        var mesh = new Mesh { name = name };
-        mesh.SetVertices(vertices);
-        mesh.SetNormals(normals);
-        mesh.SetIndices(indices, MeshTopology.Triangles, 0, false);
-        mesh.SetUVs(0, uvs);
+        AliasModel aliasModel = new AliasModel();
         
-        CreateBlendShapes(mesh, vertices, normals, header, poseVertices);
+        Mesh mesh;
+        string animName = null;
+        int startFrame = 0;
+        for (int frameIdx = 0; frameIdx < header.numFrames; ++frameIdx)
+        {
+            string frameName = AliasModel.AnimationRegex.Match(header.frames[frameIdx].name).Value;
+            if (animName == null)
+            {
+                animName = frameName;
+                continue;
+            }
 
-        mesh.Optimize();    // This ensures that triangles will be properly fused and organized in the best possible way
-        mesh.RecalculateBounds();
-        mesh.UploadMeshData(true);
+            if (frameName != animName)
+            {
+                // New animation sequence; convert the previous sequence into a blend shape animation
+                mesh = CreateAnimatedMesh(header, poseVertices, indices, uvs, animName, startFrame, frameIdx);
+                aliasModel.AddAnimation(startFrame, mesh);
+                
+                animName = frameName;
+                startFrame = frameIdx;
+            }
+        }
+        
+        mesh = CreateAnimatedMesh(header, poseVertices, indices, uvs, animName, startFrame, header.numFrames);
+        aliasModel.AddAnimation(startFrame, mesh);
 
         var go = new GameObject(System.IO.Path.GetFileNameWithoutExtension(name));
         go.transform.SetPositionAndRotation(new Vector3(xPos, 0, 0), Quaternion.Euler(-90, 90, 0));
@@ -46,7 +61,9 @@ public partial class RenderModule
             mr.receiveShadows = false;
             mr.lightProbeUsage = LightProbeUsage.Off;
             mr.reflectionProbeUsage = ReflectionProbeUsage.Off;
-            go.AddComponent<AliasModelAnimator>();
+            
+            var animator = go.AddComponent<AliasModelAnimator>();
+            animator.aliasModel = aliasModel;
         }
         else
         {
@@ -109,9 +126,29 @@ public partial class RenderModule
         }
     }
 
+    private static Mesh CreateAnimatedMesh(
+        QAliasHeader header, QTriVertex[][] poseVertices, ushort[] indices, Vector2[] uvs,
+        string animationName, int startFrame, int endFrame)
+    {
+        ConvertVertices(header, poseVertices[startFrame], out var baseVertices, out var baseNormals);
+        
+        var mesh = new Mesh { name = animationName };
+        mesh.SetVertices(baseVertices);
+        mesh.SetNormals(baseNormals);
+
+        CreateBlendShapes(mesh, animationName, baseVertices, baseNormals, header, poseVertices, startFrame, endFrame);
+        
+        mesh.SetIndices(indices, MeshTopology.Triangles, 0, false);
+        mesh.SetUVs(0, uvs);
+        mesh.Optimize();
+        mesh.RecalculateBounds();
+        mesh.UploadMeshData(true);
+        return mesh;
+    }
+
     private static void CreateBlendShapes(
-        Mesh mesh, Vector3[] baseVertices, Vector3[] baseNormals,
-        QAliasHeader header, QTriVertex[][] poseVertices)
+        Mesh mesh, string animName, Vector3[] baseVertices, Vector3[] baseNormals,
+        QAliasHeader header, QTriVertex[][] poseVertices, int startFrame, int endFrame)
     {
         var deltaVertices = new Vector3[header.numVerts];
         var deltaNormals = new Vector3[header.numVerts];
@@ -119,9 +156,12 @@ public partial class RenderModule
         Vector3 scale = header.scale.ToVector3();
         Vector3 origin = header.scaleOrigin.ToVector3();
         
-        // Frame 0 is the base pose, so we start with frame 1
-        for (int frameIdx = 1; frameIdx < header.numFrames; ++frameIdx)
+        int numFrames = endFrame - startFrame;
+        
+        // Repeat the first frame at the end, so we can smoothly animate the entire cycle and loop the animation without any breaks.
+        for (int index = 1; index <= numFrames; ++index)
         {
+            int frameIdx = startFrame + index % numFrames;
             var poseVerts = poseVertices[frameIdx];
             
             for (int vertIdx = 0; vertIdx < header.numVerts; ++vertIdx)
@@ -131,7 +171,7 @@ public partial class RenderModule
                 deltaNormals[vertIdx] = QLightNormals.Get(poseVerts[vertIdx].lightNormalIndex) - baseNormals[vertIdx];
             }
             
-            mesh.AddBlendShapeFrame(mesh.name, (float)frameIdx / (header.numFrames-1), deltaVertices, deltaNormals, null);
+            mesh.AddBlendShapeFrame(animName, (float)index / numFrames, deltaVertices, deltaNormals, null);
         }
     }
 }